Starting phenix.real_space_refine on Sun Oct 25 04:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ss_75440/10_2026/10ss_75440.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ss_75440/10_2026/10ss_75440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10ss_75440/10_2026/10ss_75440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ss_75440/10_2026/10ss_75440.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10ss_75440/10_2026/10ss_75440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ss_75440/10_2026/10ss_75440.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 sd= 0.440 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 9926 2.51 5 N 2702 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15946 Number of models: 1 Model: "" Number of chains: 14 Chain: "a" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "b" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "c" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "d" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "e" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "f" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "g" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "A" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "B" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "C" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "D" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "E" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "F" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain: "G" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1139 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 150} Time building chain proxies: 3.15, per 1000 atoms: 0.20 Number of scatterers: 15946 At special positions: 0 Unit cell: (83.25, 113.22, 239.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 3290 8.00 N 2702 7.00 C 9926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS a 37 " - pdb=" SG CYS a 78 " distance=2.03 Simple disulfide: pdb=" SG CYS b 37 " - pdb=" SG CYS b 78 " distance=2.03 Simple disulfide: pdb=" SG CYS c 37 " - pdb=" SG CYS c 78 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 78 " distance=2.03 Simple disulfide: pdb=" SG CYS e 37 " - pdb=" SG CYS e 78 " distance=2.03 Simple disulfide: pdb=" SG CYS f 37 " - pdb=" SG CYS f 78 " distance=2.03 Simple disulfide: pdb=" SG CYS g 37 " - pdb=" SG CYS g 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 37 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 37 " - pdb=" SG CYS G 78 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 713.5 milliseconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 45 sheets defined 0.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'a' and resid 47 through 50 removed outlier: 3.660A pdb=" N THR b 27 " --> pdb=" O PHE a 47 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN b 29 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER a 170 " --> pdb=" O PHE b 28 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS a 173 " --> pdb=" O GLU a 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 69 through 70 removed outlier: 3.502A pdb=" N LEU a 114 " --> pdb=" O LEU a 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 73 through 76 removed outlier: 3.756A pdb=" N LEU a 75 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 38 through 39 removed outlier: 3.592A pdb=" N ILE b 73 " --> pdb=" O LEU b 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 47 through 50 removed outlier: 3.620A pdb=" N ASN c 29 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS b 173 " --> pdb=" O GLU b 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 123 through 124 removed outlier: 4.637A pdb=" N LEU b 116 " --> pdb=" O LEU b 124 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ASN b 111 " --> pdb=" O THR b 160 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR b 160 " --> pdb=" O ASN b 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 38 through 39 removed outlier: 3.612A pdb=" N LEU c 75 " --> pdb=" O ALA c 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 47 through 50 Processing sheet with id=AA9, first strand: chain 'c' and resid 69 through 70 removed outlier: 3.882A pdb=" N LEU c 114 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'd' and resid 38 through 39 removed outlier: 3.579A pdb=" N ILE d 73 " --> pdb=" O LEU d 151 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU d 75 " --> pdb=" O ALA d 149 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA d 149 " --> pdb=" O LEU d 75 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'd' and resid 47 through 49 removed outlier: 3.786A pdb=" N ASN e 29 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL d 168 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS d 173 " --> pdb=" O GLU d 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 112 through 117 Processing sheet with id=AB5, first strand: chain 'e' and resid 38 through 39 Processing sheet with id=AB6, first strand: chain 'e' and resid 47 through 50 removed outlier: 3.552A pdb=" N ASN f 29 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS e 173 " --> pdb=" O GLU e 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 112 through 117 Processing sheet with id=AB8, first strand: chain 'f' and resid 38 through 39 removed outlier: 3.509A pdb=" N THR f 76 " --> pdb=" O THR f 38 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU f 75 " --> pdb=" O ALA f 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'f' and resid 47 through 50 removed outlier: 4.288A pdb=" N LYS f 173 " --> pdb=" O GLU f 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR f 175 " --> pdb=" O TYR f 86 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL f 141 " --> pdb=" O VAL f 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'f' and resid 100 through 101 removed outlier: 3.575A pdb=" N LEU f 117 " --> pdb=" O TYR f 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'g' and resid 38 through 39 removed outlier: 3.690A pdb=" N ILE g 73 " --> pdb=" O LEU g 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU g 75 " --> pdb=" O ALA g 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 69 through 70 Processing sheet with id=AC4, first strand: chain 'g' and resid 141 through 142 removed outlier: 4.972A pdb=" N LYS g 173 " --> pdb=" O GLU g 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.411A pdb=" N PHE A 47 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN B 29 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 49 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N LYS B 31 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS A 173 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.411A pdb=" N PHE A 47 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN B 29 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 49 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N LYS B 31 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 168 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.503A pdb=" N LEU A 114 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39 removed outlier: 3.614A pdb=" N THR B 38 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 76 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.112A pdb=" N PHE B 47 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASN C 29 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 49 " --> pdb=" O ASN C 29 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS C 31 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS B 173 " --> pdb=" O GLU B 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.581A pdb=" N LEU B 117 " --> pdb=" O TYR B 154 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 38 through 39 removed outlier: 3.689A pdb=" N LEU C 75 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 149 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.704A pdb=" N PHE C 47 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASN D 29 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C 49 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LYS D 31 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS C 173 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 112 through 117 Processing sheet with id=AD6, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.063A pdb=" N THR D 38 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR D 76 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 73 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 151 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 75 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 47 through 50 removed outlier: 3.535A pdb=" N SER D 170 " --> pdb=" O PHE E 28 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 69 through 70 removed outlier: 3.716A pdb=" N LEU D 114 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 141 through 142 removed outlier: 3.538A pdb=" N VAL D 141 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.541A pdb=" N ILE E 73 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 47 through 50 removed outlier: 3.584A pdb=" N THR F 27 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 29 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS E 173 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 69 through 70 Processing sheet with id=AE4, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AE5, first strand: chain 'F' and resid 47 through 50 removed outlier: 4.060A pdb=" N THR G 27 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL F 49 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN G 29 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS F 173 " --> pdb=" O GLU F 88 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 100 through 101 removed outlier: 3.602A pdb=" N LEU F 114 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 117 " --> pdb=" O TYR F 154 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'G' and resid 141 through 142 removed outlier: 3.583A pdb=" N VAL G 141 " --> pdb=" O VAL G 83 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL G 83 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS G 173 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 112 through 117 354 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5348 1.35 - 1.47: 3945 1.47 - 1.59: 6904 1.59 - 1.71: 1 1.71 - 1.83: 28 Bond restraints: 16226 Sorted by residual: bond pdb=" CB PRO B 165 " pdb=" CG PRO B 165 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.07e+00 bond pdb=" CG PRO B 165 " pdb=" CD PRO B 165 " ideal model delta sigma weight residual 1.503 1.558 -0.055 3.40e-02 8.65e+02 2.63e+00 bond pdb=" CB PRO D 42 " pdb=" CG PRO D 42 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.03e+00 bond pdb=" CB ASN D 110 " pdb=" CG ASN D 110 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.64e+00 bond pdb=" CB GLU D 88 " pdb=" CG GLU D 88 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 ... (remaining 16221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 21749 1.93 - 3.87: 412 3.87 - 5.80: 31 5.80 - 7.73: 10 7.73 - 9.67: 2 Bond angle restraints: 22204 Sorted by residual: angle pdb=" CA PRO B 165 " pdb=" N PRO B 165 " pdb=" CD PRO B 165 " ideal model delta sigma weight residual 112.00 102.50 9.50 1.40e+00 5.10e-01 4.61e+01 angle pdb=" CA LYS D 31 " pdb=" CB LYS D 31 " pdb=" CG LYS D 31 " ideal model delta sigma weight residual 114.10 121.16 -7.06 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CA GLU D 88 " pdb=" CB GLU D 88 " pdb=" CG GLU D 88 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CA GLU a 88 " pdb=" CB GLU a 88 " pdb=" CG GLU a 88 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB LYS A 77 " pdb=" CG LYS A 77 " pdb=" CD LYS A 77 " ideal model delta sigma weight residual 111.30 119.00 -7.70 2.30e+00 1.89e-01 1.12e+01 ... (remaining 22199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8305 17.72 - 35.44: 925 35.44 - 53.17: 232 53.17 - 70.89: 38 70.89 - 88.61: 20 Dihedral angle restraints: 9520 sinusoidal: 3262 harmonic: 6258 Sorted by residual: dihedral pdb=" CB CYS F 37 " pdb=" SG CYS F 37 " pdb=" SG CYS F 78 " pdb=" CB CYS F 78 " ideal model delta sinusoidal sigma weight residual 93.00 14.25 78.75 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS g 37 " pdb=" SG CYS g 37 " pdb=" SG CYS g 78 " pdb=" CB CYS g 78 " ideal model delta sinusoidal sigma weight residual 93.00 21.82 71.18 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS D 37 " pdb=" SG CYS D 37 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual 93.00 156.13 -63.13 1 1.00e+01 1.00e-02 5.26e+01 ... (remaining 9517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1902 0.036 - 0.072: 445 0.072 - 0.108: 191 0.108 - 0.144: 92 0.144 - 0.180: 2 Chirality restraints: 2632 Sorted by residual: chirality pdb=" CB ILE F 73 " pdb=" CA ILE F 73 " pdb=" CG1 ILE F 73 " pdb=" CG2 ILE F 73 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB ILE a 126 " pdb=" CA ILE a 126 " pdb=" CG1 ILE a 126 " pdb=" CG2 ILE a 126 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA PRO B 165 " pdb=" N PRO B 165 " pdb=" C PRO B 165 " pdb=" CB PRO B 165 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 2629 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 41 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO D 42 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 164 " 0.065 5.00e-02 4.00e+02 9.27e-02 1.38e+01 pdb=" N PRO B 165 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR f 41 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.92e+00 pdb=" N PRO f 42 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO f 42 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO f 42 " 0.039 5.00e-02 4.00e+02 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 733 2.70 - 3.25: 14671 3.25 - 3.80: 22757 3.80 - 4.35: 25562 4.35 - 4.90: 46933 Nonbonded interactions: 110656 Sorted by model distance: nonbonded pdb=" OD1 ASN D 111 " pdb=" OG1 THR D 160 " model vdw 2.156 3.040 nonbonded pdb=" O GLN c 103 " pdb=" OG1 THR c 169 " model vdw 2.191 3.040 nonbonded pdb=" OG SER A 55 " pdb=" O LYS B 35 " model vdw 2.205 3.040 nonbonded pdb=" O ARG d 68 " pdb=" OH TYR e 86 " model vdw 2.212 3.040 nonbonded pdb=" O GLN B 103 " pdb=" OG1 THR B 169 " model vdw 2.213 3.040 ... (remaining 110651 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.120 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.860 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.020 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 16240 Z= 0.145 Angle : 0.643 9.669 22232 Z= 0.363 Chirality : 0.042 0.180 2632 Planarity : 0.006 0.102 2940 Dihedral : 16.008 88.609 5502 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.36 % Allowed : 26.47 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -2.40 (0.23), residues: 392 loop : -1.58 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 99 TYR 0.020 0.001 TYR D 157 PHE 0.015 0.001 PHE a 123 TRP 0.013 0.002 TRP D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (16226) covalent geometry : angle 0.63860 / 0.36 (22204) SS BOND : bond 0.00143 / 0.09 ( 14) SS BOND : angle 2.14036 / 1.39 ( 28) hydrogen bonds : bond 0.31885 / 21.39 ( 354) hydrogen bonds : angle 11.15733 / 7.55 ( 795) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: g 88 GLU cc_start: 0.8756 (mp0) cc_final: 0.8379 (mp0) REVERT: g 94 ASP cc_start: 0.9013 (t0) cc_final: 0.8773 (m-30) REVERT: B 77 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8355 (pttt) REVERT: G 117 LEU cc_start: 0.8265 (mp) cc_final: 0.7971 (mp) outliers start: 6 outliers final: 5 residues processed: 175 average time/residue: 0.1102 time to fit residues: 29.3522 Evaluate side-chains 157 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain A residue 179 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 0.0270 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0010 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 1.1848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 120 ASN a 122 GLN a 137 ASN d 120 ASN d 137 ASN e 139 GLN f 133 GLN C 120 ASN C 137 ASN D 152 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.045556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.041191 restraints weight = 77295.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.042260 restraints weight = 37786.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.042957 restraints weight = 21996.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.043418 restraints weight = 14402.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.043743 restraints weight = 10304.165| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16240 Z= 0.137 Angle : 0.577 7.356 22232 Z= 0.310 Chirality : 0.043 0.156 2632 Planarity : 0.005 0.071 2940 Dihedral : 4.994 33.784 2332 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.64 % Allowed : 24.79 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -2.23 (0.18), residues: 616 loop : -1.31 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG d 68 TYR 0.017 0.002 TYR D 157 PHE 0.017 0.002 PHE d 28 TRP 0.011 0.002 TRP A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16226) covalent geometry : angle 0.57095 / 0.31 (22204) SS BOND : bond 0.00224 / 0.14 ( 14) SS BOND : angle 2.41454 / 1.52 ( 28) hydrogen bonds : bond 0.03315 / 2.24 ( 354) hydrogen bonds : angle 7.38546 / 5.00 ( 795) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: f 75 LEU cc_start: 0.8938 (tp) cc_final: 0.8566 (tp) REVERT: g 88 GLU cc_start: 0.8779 (mp0) cc_final: 0.8345 (mp0) REVERT: g 92 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8744 (t) REVERT: g 103 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8319 (mm-40) REVERT: g 123 PHE cc_start: 0.7799 (t80) cc_final: 0.7557 (t80) REVERT: g 150 ASP cc_start: 0.9035 (m-30) cc_final: 0.8830 (m-30) REVERT: A 53 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 78 CYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6611 (m) REVERT: E 122 GLN cc_start: 0.7417 (mp10) cc_final: 0.7168 (mp10) REVERT: G 115 GLN cc_start: 0.7950 (mt0) cc_final: 0.7599 (tt0) REVERT: G 117 LEU cc_start: 0.8331 (mp) cc_final: 0.7953 (mp) REVERT: G 154 TYR cc_start: 0.8802 (m-80) cc_final: 0.8360 (m-80) outliers start: 44 outliers final: 19 residues processed: 205 average time/residue: 0.1065 time to fit residues: 33.7761 Evaluate side-chains 175 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 92 THR Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [116, 76, 57, 82, 53, 122, 190, 144, 123, 10, 87] chunk 116 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 115 GLN b 137 ASN g 120 ASN A 120 ASN C 137 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN G 120 ASN G 122 GLN G 137 ASN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.042077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.037824 restraints weight = 80686.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.038852 restraints weight = 38991.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.039517 restraints weight = 22548.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.039972 restraints weight = 14759.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.040278 restraints weight = 10551.128| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16240 Z= 0.250 Angle : 0.716 10.451 22232 Z= 0.388 Chirality : 0.045 0.177 2632 Planarity : 0.006 0.060 2940 Dihedral : 5.941 37.900 2327 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.86 % Allowed : 24.31 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -2.26 (0.18), residues: 616 loop : -1.58 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 68 TYR 0.026 0.003 TYR a 154 PHE 0.025 0.003 PHE d 71 TRP 0.015 0.002 TRP c 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (16226) covalent geometry : angle 0.71050 / 0.39 (22204) SS BOND : bond 0.00379 / 0.22 ( 14) SS BOND : angle 2.61168 / 1.67 ( 28) hydrogen bonds : bond 0.04329 / 2.89 ( 354) hydrogen bonds : angle 7.21938 / 4.92 ( 795) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 152 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: f 47 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7691 (m-10) REVERT: f 71 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: f 114 LEU cc_start: 0.8718 (mp) cc_final: 0.8483 (mt) REVERT: g 88 GLU cc_start: 0.8915 (mp0) cc_final: 0.8569 (mp0) REVERT: B 78 CYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6751 (m) REVERT: D 146 ASP cc_start: 0.8163 (p0) cc_final: 0.7906 (p0) REVERT: E 71 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: E 122 GLN cc_start: 0.7672 (mp10) cc_final: 0.7363 (mp10) outliers start: 81 outliers final: 47 residues processed: 217 average time/residue: 0.1118 time to fit residues: 37.1993 Evaluate side-chains 192 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 140 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain a residue 123 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain c residue 179 ASN Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain d residue 177 ILE Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 47 PHE Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [86, 58, 46, 79, 206, 30, 168, 70, 14, 75, 96] chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN c 139 GLN d 111 ASN f 135 GLN A 113 GLN A 179 ASN B 120 ASN C 115 GLN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.040700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.036578 restraints weight = 80968.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.037580 restraints weight = 38719.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.038232 restraints weight = 22266.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.038661 restraints weight = 14514.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.038964 restraints weight = 10386.843| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 16240 Z= 0.291 Angle : 0.776 12.792 22232 Z= 0.420 Chirality : 0.047 0.193 2632 Planarity : 0.006 0.061 2940 Dihedral : 6.492 38.525 2325 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 5.28 % Allowed : 25.45 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.15), residues: 2170 helix: None (None), residues: 0 sheet: -2.04 (0.21), residues: 476 loop : -1.96 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 68 TYR 0.030 0.003 TYR a 154 PHE 0.030 0.003 PHE d 71 TRP 0.018 0.003 TRP a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.29 (16226) covalent geometry : angle 0.76958 / 0.42 (22204) SS BOND : bond 0.00449 / 0.26 ( 14) SS BOND : angle 2.85993 / 1.84 ( 28) hydrogen bonds : bond 0.04583 / 3.05 ( 354) hydrogen bonds : angle 7.19907 / 4.91 ( 795) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 147 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.6982 (m-80) REVERT: a 156 GLU cc_start: 0.8334 (pp20) cc_final: 0.7740 (pp20) REVERT: b 103 GLN cc_start: 0.8132 (tt0) cc_final: 0.7930 (tt0) REVERT: e 88 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: f 47 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: f 71 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: g 71 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 77 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8413 (pttt) REVERT: F 99 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7627 (mtm-85) REVERT: G 45 LYS cc_start: 0.4542 (tptt) cc_final: 0.3665 (tptt) REVERT: G 115 GLN cc_start: 0.8230 (mt0) cc_final: 0.8019 (mt0) outliers start: 88 outliers final: 59 residues processed: 218 average time/residue: 0.1110 time to fit residues: 36.8740 Evaluate side-chains 197 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 133 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain a residue 123 PHE Chi-restraints excluded: chain a residue 179 ASN Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 110 ASN Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 179 ASN Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 111 ASN Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain d residue 177 ILE Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 88 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 47 PHE Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [106, 119, 4, 55, 68, 81, 162, 204, 143, 9, 24] chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 162 optimal weight: 0.0570 chunk 204 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 ASN d 111 ASN f 135 GLN A 179 ASN B 103 GLN E 122 GLN F 139 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.041318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.037189 restraints weight = 80178.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.038202 restraints weight = 38130.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.038856 restraints weight = 21914.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.039294 restraints weight = 14249.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.039594 restraints weight = 10159.438| |-----------------------------------------------------------------------------| r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16240 Z= 0.226 Angle : 0.707 12.198 22232 Z= 0.380 Chirality : 0.045 0.230 2632 Planarity : 0.006 0.064 2940 Dihedral : 6.145 38.428 2325 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 5.22 % Allowed : 25.87 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.15), residues: 2170 helix: None (None), residues: 0 sheet: -2.05 (0.21), residues: 476 loop : -1.95 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 68 TYR 0.025 0.002 TYR a 154 PHE 0.022 0.002 PHE d 71 TRP 0.014 0.002 TRP a 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.23 (16226) covalent geometry : angle 0.70087 / 0.38 (22204) SS BOND : bond 0.00359 / 0.22 ( 14) SS BOND : angle 2.72647 / 1.75 ( 28) hydrogen bonds : bond 0.03915 / 2.62 ( 354) hydrogen bonds : angle 6.92189 / 4.72 ( 795) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 147 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: a 156 GLU cc_start: 0.8246 (pp20) cc_final: 0.7648 (pp20) REVERT: e 88 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.5888 (mt-10) REVERT: f 47 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7608 (m-10) REVERT: f 71 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7660 (m-10) REVERT: g 71 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: g 88 GLU cc_start: 0.8879 (mp0) cc_final: 0.8490 (mp0) REVERT: g 120 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (p0) REVERT: B 77 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8433 (pttt) REVERT: G 115 GLN cc_start: 0.8255 (mt0) cc_final: 0.7992 (mt0) outliers start: 87 outliers final: 58 residues processed: 215 average time/residue: 0.1112 time to fit residues: 36.6816 Evaluate side-chains 201 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 137 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain a residue 123 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 110 ASN Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 179 ASN Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 94 ASP Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 88 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 47 PHE Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 120 ASN Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [208, 170, 182, 96, 69, 44, 12, 17, 91, 113, 2] chunk 208 optimal weight: 3.9990 chunk 170 optimal weight: 0.0470 chunk 182 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 12 optimal weight: 0.0030 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 103 GLN C 115 GLN E 122 GLN E 135 GLN F 139 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.043983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.039711 restraints weight = 79006.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.040764 restraints weight = 38156.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.041445 restraints weight = 22027.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.041874 restraints weight = 14358.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.042202 restraints weight = 10383.010| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16240 Z= 0.119 Angle : 0.579 11.846 22232 Z= 0.305 Chirality : 0.043 0.179 2632 Planarity : 0.005 0.057 2940 Dihedral : 5.140 36.292 2325 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.44 % Allowed : 26.59 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -1.97 (0.21), residues: 476 loop : -1.77 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 99 TYR 0.014 0.001 TYR C 157 PHE 0.013 0.001 PHE d 28 TRP 0.016 0.002 TRP b 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16226) covalent geometry : angle 0.57403 / 0.30 (22204) SS BOND : bond 0.00553 / 0.30 ( 14) SS BOND : angle 2.17850 / 1.36 ( 28) hydrogen bonds : bond 0.02548 / 1.73 ( 354) hydrogen bonds : angle 6.33227 / 4.27 ( 795) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 88 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7764 (tm-30) REVERT: a 156 GLU cc_start: 0.8055 (pp20) cc_final: 0.7518 (pp20) REVERT: e 126 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6765 (mt) REVERT: f 71 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: g 88 GLU cc_start: 0.8728 (mp0) cc_final: 0.8295 (mp0) REVERT: A 53 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8217 (m) REVERT: B 122 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: C 78 CYS cc_start: 0.5757 (m) cc_final: 0.5556 (m) REVERT: G 115 GLN cc_start: 0.8180 (mt0) cc_final: 0.7969 (mt0) outliers start: 74 outliers final: 45 residues processed: 221 average time/residue: 0.1035 time to fit residues: 35.3153 Evaluate side-chains 201 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 126 ILE Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 28 PHE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 71 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [107, 73, 56, 152, 138, 10, 55, 26, 170, 180, 15] chunk 107 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 170 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... g 102 ASN A 179 ASN E 122 GLN F 139 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.043096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.038892 restraints weight = 78576.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.039923 restraints weight = 37832.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.040595 restraints weight = 21779.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.041044 restraints weight = 14170.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.041343 restraints weight = 10102.459| |-----------------------------------------------------------------------------| r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16240 Z= 0.153 Angle : 0.617 11.948 22232 Z= 0.327 Chirality : 0.043 0.183 2632 Planarity : 0.005 0.053 2940 Dihedral : 5.226 36.527 2325 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.14 % Allowed : 26.95 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -1.90 (0.21), residues: 476 loop : -1.76 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 99 TYR 0.018 0.002 TYR C 157 PHE 0.017 0.002 PHE g 28 TRP 0.009 0.002 TRP b 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (16226) covalent geometry : angle 0.61272 / 0.33 (22204) SS BOND : bond 0.00227 / 0.14 ( 14) SS BOND : angle 2.20195 / 1.42 ( 28) hydrogen bonds : bond 0.03042 / 2.06 ( 354) hydrogen bonds : angle 6.34325 / 4.29 ( 795) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: a 156 GLU cc_start: 0.8049 (pp20) cc_final: 0.7524 (pp20) REVERT: b 122 GLN cc_start: 0.8218 (mt0) cc_final: 0.7998 (mt0) REVERT: e 47 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7370 (m-10) REVERT: e 88 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.5932 (mt-10) REVERT: f 71 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: g 88 GLU cc_start: 0.8745 (mp0) cc_final: 0.8320 (mp0) REVERT: A 53 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8168 (m) REVERT: C 78 CYS cc_start: 0.5890 (m) cc_final: 0.5681 (m) outliers start: 69 outliers final: 45 residues processed: 208 average time/residue: 0.1085 time to fit residues: 34.6928 Evaluate side-chains 201 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 88 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 28 PHE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [189, 192, 143, 146, 17, 89, 40, 193, 94, 110, 144] chunk 189 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 146 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN B 103 GLN E 122 GLN F 139 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.043307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.039079 restraints weight = 79099.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.040121 restraints weight = 38055.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.040796 restraints weight = 21917.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.041231 restraints weight = 14294.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.041552 restraints weight = 10293.194| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16240 Z= 0.149 Angle : 0.618 13.758 22232 Z= 0.327 Chirality : 0.044 0.205 2632 Planarity : 0.005 0.053 2940 Dihedral : 5.198 36.637 2325 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.50 % Allowed : 26.77 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -1.88 (0.21), residues: 476 loop : -1.73 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 99 TYR 0.018 0.002 TYR B 86 PHE 0.016 0.002 PHE g 28 TRP 0.011 0.001 TRP b 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (16226) covalent geometry : angle 0.61368 / 0.33 (22204) SS BOND : bond 0.00225 / 0.14 ( 14) SS BOND : angle 2.18135 / 1.39 ( 28) hydrogen bonds : bond 0.02945 / 2.00 ( 354) hydrogen bonds : angle 6.32296 / 4.28 ( 795) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 152 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: a 156 GLU cc_start: 0.8015 (pp20) cc_final: 0.7508 (pp20) REVERT: b 122 GLN cc_start: 0.8207 (mt0) cc_final: 0.7964 (mt0) REVERT: e 47 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: e 88 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.5936 (mt-10) REVERT: f 71 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: g 88 GLU cc_start: 0.8760 (mp0) cc_final: 0.8333 (mp0) REVERT: g 123 PHE cc_start: 0.7856 (t80) cc_final: 0.7614 (t80) REVERT: A 53 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8155 (m) REVERT: B 122 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: G 45 LYS cc_start: 0.4995 (tptt) cc_final: 0.4114 (tptt) outliers start: 75 outliers final: 53 residues processed: 213 average time/residue: 0.1076 time to fit residues: 35.0844 Evaluate side-chains 206 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 88 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 28 PHE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [104, 26, 77, 14, 76, 49, 115, 87, 100, 177, 181] chunk 104 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... e 139 GLN A 179 ASN F 139 GLN G 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.043070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.038856 restraints weight = 79260.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.039896 restraints weight = 38052.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.040566 restraints weight = 21929.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.041018 restraints weight = 14286.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.041327 restraints weight = 10195.120| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16240 Z= 0.161 Angle : 0.638 12.506 22232 Z= 0.337 Chirality : 0.044 0.209 2632 Planarity : 0.005 0.054 2940 Dihedral : 5.248 36.819 2325 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 4.02 % Allowed : 27.01 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -1.89 (0.21), residues: 476 loop : -1.74 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 99 TYR 0.017 0.002 TYR C 157 PHE 0.017 0.002 PHE g 28 TRP 0.010 0.001 TRP b 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (16226) covalent geometry : angle 0.63349 / 0.33 (22204) SS BOND : bond 0.00290 / 0.18 ( 14) SS BOND : angle 2.16359 / 1.41 ( 28) hydrogen bonds : bond 0.03065 / 2.07 ( 354) hydrogen bonds : angle 6.33803 / 4.30 ( 795) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 147 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: a 156 GLU cc_start: 0.8023 (pp20) cc_final: 0.7505 (pp20) REVERT: b 122 GLN cc_start: 0.8181 (mt0) cc_final: 0.7933 (mt0) REVERT: e 47 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7314 (m-10) REVERT: e 88 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.5968 (mt-10) REVERT: f 71 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7383 (m-80) REVERT: g 75 LEU cc_start: 0.8512 (pt) cc_final: 0.8273 (pt) REVERT: g 88 GLU cc_start: 0.8786 (mp0) cc_final: 0.8389 (mp0) REVERT: g 123 PHE cc_start: 0.7837 (t80) cc_final: 0.7590 (t80) REVERT: A 53 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 122 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: G 45 LYS cc_start: 0.4882 (tptt) cc_final: 0.4117 (tptt) outliers start: 67 outliers final: 57 residues processed: 203 average time/residue: 0.1085 time to fit residues: 34.3958 Evaluate side-chains 209 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 146 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 88 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 28 PHE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [151, 154, 147, 80, 161, 1, 178, 179, 105, 201, 160] chunk 151 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 135 GLN A 179 ASN B 103 GLN E 122 GLN E 135 GLN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.041634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.037504 restraints weight = 79440.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.038524 restraints weight = 37945.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.039179 restraints weight = 21796.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.039617 restraints weight = 14187.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.039916 restraints weight = 10120.657| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16240 Z= 0.221 Angle : 0.709 13.428 22232 Z= 0.378 Chirality : 0.045 0.210 2632 Planarity : 0.005 0.058 2940 Dihedral : 5.751 37.726 2325 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 4.26 % Allowed : 27.13 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -1.92 (0.21), residues: 476 loop : -1.83 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 99 TYR 0.024 0.002 TYR a 154 PHE 0.022 0.002 PHE g 28 TRP 0.010 0.002 TRP c 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (16226) covalent geometry : angle 0.70385 / 0.38 (22204) SS BOND : bond 0.00339 / 0.21 ( 14) SS BOND : angle 2.42258 / 1.57 ( 28) hydrogen bonds : bond 0.03783 / 2.55 ( 354) hydrogen bonds : angle 6.62476 / 4.50 ( 795) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 144 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 71 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: a 156 GLU cc_start: 0.8096 (pp20) cc_final: 0.7585 (pp20) REVERT: b 122 GLN cc_start: 0.8215 (mt0) cc_final: 0.7987 (mt0) REVERT: e 47 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: e 88 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6009 (mt-10) REVERT: f 71 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: g 71 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: g 88 GLU cc_start: 0.8817 (mp0) cc_final: 0.8416 (mp0) REVERT: A 53 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8146 (m) REVERT: B 122 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: G 45 LYS cc_start: 0.4946 (tptt) cc_final: 0.4206 (tptt) outliers start: 71 outliers final: 60 residues processed: 203 average time/residue: 0.1087 time to fit residues: 33.9277 Evaluate side-chains 210 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 143 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 37 CYS Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 71 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 107 ASN Chi-restraints excluded: chain a residue 116 LEU Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 71 PHE Chi-restraints excluded: chain c residue 47 PHE Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 176 ILE Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 138 SER Chi-restraints excluded: chain d residue 145 THR Chi-restraints excluded: chain e residue 25 THR Chi-restraints excluded: chain e residue 39 ILE Chi-restraints excluded: chain e residue 47 PHE Chi-restraints excluded: chain e residue 88 GLU Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain f residue 71 PHE Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 172 VAL Chi-restraints excluded: chain g residue 28 PHE Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 47 PHE Chi-restraints excluded: chain g residue 71 PHE Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain g residue 172 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 173 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 71 PHE Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 102 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: [123, 138, 193, 107, 171, 165, 24, 151, 69, 87, 170] chunk 123 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 107 optimal weight: 0.0050 chunk 171 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 179 ASN A 179 ASN B 103 GLN D 74 ASN F 139 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.042906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.038757 restraints weight = 78612.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.039784 restraints weight = 37641.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.040449 restraints weight = 21642.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.040900 restraints weight = 14070.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.041199 restraints weight = 10006.251| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16240 Z= 0.150 Angle : 0.630 12.354 22232 Z= 0.334 Chirality : 0.044 0.189 2632 Planarity : 0.005 0.058 2940 Dihedral : 5.361 37.044 2325 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.02 % Allowed : 27.37 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.16), residues: 2170 helix: None (None), residues: 0 sheet: -1.92 (0.21), residues: 476 loop : -1.77 (0.13), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 99 TYR 0.017 0.002 TYR C 157 PHE 0.016 0.002 PHE g 28 TRP 0.013 0.002 TRP b 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (16226) covalent geometry : angle 0.62609 / 0.33 (22204) SS BOND : bond 0.00230 / 0.14 ( 14) SS BOND : angle 2.13650 / 1.39 ( 28) hydrogen bonds : bond 0.02955 / 2.00 ( 354) hydrogen bonds : angle 6.40452 / 4.34 ( 795) =============================================================================== Job complete usr+sys time: 1960.47 seconds wall clock time: 34 minutes 59.08 seconds (2099.08 seconds total)