Starting phenix.real_space_refine on Sat Aug 23 16:35:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghs_40049/08_2025/8ghs_40049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghs_40049/08_2025/8ghs_40049.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/8ghs_40049/08_2025/8ghs_40049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghs_40049/08_2025/8ghs_40049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ghs_40049/08_2025/8ghs_40049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghs_40049/08_2025/8ghs_40049.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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 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 60 5.16 5 C 8911 2.51 5 N 2252 2.21 5 O 2503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13726 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1163 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 12, 'TRANS': 133} Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "C" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "F" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1163 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 12, 'TRANS': 133} Chain: "E" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "H" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1188 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 12, 'TRANS': 138} Chain: "G" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "J" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "I" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "L" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1156 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "K" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Time building chain proxies: 2.91, per 1000 atoms: 0.21 Number of scatterers: 13726 At special positions: 0 Unit cell: (180.42, 180.42, 73.72, 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 60 16.00 O 2503 8.00 N 2252 7.00 C 8911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS C 61 " distance=2.04 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS E 61 " distance=2.05 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS I 61 " distance=2.04 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS K 61 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 430.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.832A pdb=" N GLU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 removed outlier: 3.723A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 38 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.720A pdb=" N THR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 111 removed outlier: 3.654A pdb=" N VAL B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.886A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 12 through 18 removed outlier: 3.515A pdb=" N PHE A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 removed outlier: 7.432A pdb=" N ASP A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.932A pdb=" N THR A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.694A pdb=" N ARG A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.737A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 9 removed outlier: 4.017A pdb=" N GLU D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 9 " --> pdb=" O PRO D 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4 through 9' Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 26 through 44 removed outlier: 4.153A pdb=" N THR D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.765A pdb=" N THR D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 111 removed outlier: 3.789A pdb=" N ARG D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.939A pdb=" N THR D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.796A pdb=" N GLU C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE C 9 " --> pdb=" O PRO C 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4 through 9' Processing helix chain 'C' and resid 14 through 18 Processing helix chain 'C' and resid 26 through 44 removed outlier: 7.145A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 76 removed outlier: 3.671A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 111 removed outlier: 3.759A pdb=" N ARG C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.936A pdb=" N GLU F 8 " --> pdb=" O PRO F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 26 through 44 removed outlier: 8.540A pdb=" N ASP F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.649A pdb=" N THR F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 111 removed outlier: 3.681A pdb=" N ARG F 82 " --> pdb=" O ASP F 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.656A pdb=" N THR F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 removed outlier: 4.114A pdb=" N PHE E 9 " --> pdb=" O PRO E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 18 removed outlier: 3.546A pdb=" N PHE E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 44 removed outlier: 3.699A pdb=" N THR E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ASP E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 76 removed outlier: 3.647A pdb=" N THR E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 111 removed outlier: 3.842A pdb=" N VAL E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 Processing helix chain 'H' and resid 4 through 9 removed outlier: 3.720A pdb=" N GLU H 8 " --> pdb=" O PRO H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 17 Processing helix chain 'H' and resid 26 through 38 Processing helix chain 'H' and resid 38 through 44 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.714A pdb=" N THR H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 111 removed outlier: 4.494A pdb=" N VAL H 93 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY H 94 " --> pdb=" O ASN H 90 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS H 96 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 Processing helix chain 'H' and resid 144 through 148 removed outlier: 4.008A pdb=" N ALA H 148 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 3.701A pdb=" N GLU G 8 " --> pdb=" O PRO G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 26 through 44 removed outlier: 3.657A pdb=" N ARG G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 removed outlier: 3.895A pdb=" N THR G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 removed outlier: 3.987A pdb=" N ASN G 90 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.756A pdb=" N LYS G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 128 removed outlier: 3.543A pdb=" N ARG G 127 " --> pdb=" O GLY G 123 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 10 Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 26 through 44 removed outlier: 7.369A pdb=" N ASP J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.888A pdb=" N THR J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 111 removed outlier: 3.835A pdb=" N ARG J 82 " --> pdb=" O ASP J 78 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL J 93 " --> pdb=" O VAL J 89 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 removed outlier: 3.515A pdb=" N VAL J 115 " --> pdb=" O GLY J 111 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR J 128 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 removed outlier: 3.740A pdb=" N GLU I 8 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 26 through 44 removed outlier: 6.999A pdb=" N ASP I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA I 41 " --> pdb=" O LEU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 76 removed outlier: 3.862A pdb=" N THR I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 111 removed outlier: 4.051A pdb=" N VAL I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 removed outlier: 4.291A pdb=" N GLU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 8 removed outlier: 3.826A pdb=" N GLU L 8 " --> pdb=" O PRO L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 17 Processing helix chain 'L' and resid 26 through 44 removed outlier: 3.881A pdb=" N THR L 33 " --> pdb=" O ASP L 29 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA L 41 " --> pdb=" O LEU L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 76 removed outlier: 3.630A pdb=" N THR L 53 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 111 removed outlier: 3.943A pdb=" N VAL L 93 " --> pdb=" O VAL L 89 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY L 94 " --> pdb=" O ASN L 90 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS L 96 " --> pdb=" O ASN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.652A pdb=" N THR L 128 " --> pdb=" O VAL L 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 4.130A pdb=" N PHE K 9 " --> pdb=" O PRO K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'K' and resid 26 through 44 removed outlier: 7.003A pdb=" N ASP K 40 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ALA K 41 " --> pdb=" O LEU K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 76 removed outlier: 3.901A pdb=" N THR K 53 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 111 removed outlier: 3.646A pdb=" N VAL K 93 " --> pdb=" O VAL K 89 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY K 94 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 removed outlier: 3.532A pdb=" N VAL K 115 " --> pdb=" O GLY K 111 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG K 127 " --> pdb=" O GLY K 123 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.08 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: 4356 1.35 - 1.47: 3623 1.47 - 1.59: 6087 1.59 - 1.72: 0 1.72 - 1.84: 84 Bond restraints: 14150 Sorted by residual: bond pdb=" CA LEU I 140 " pdb=" C LEU I 140 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.42e-02 4.96e+03 1.33e+01 bond pdb=" CA SER I 141 " pdb=" C SER I 141 " ideal model delta sigma weight residual 1.520 1.488 0.031 1.16e-02 7.43e+03 7.36e+00 bond pdb=" CA ASN D 136 " pdb=" CB ASN D 136 " ideal model delta sigma weight residual 1.525 1.564 -0.039 1.47e-02 4.63e+03 7.16e+00 bond pdb=" CA ASN J 136 " pdb=" CB ASN J 136 " ideal model delta sigma weight residual 1.526 1.567 -0.041 1.53e-02 4.27e+03 7.13e+00 bond pdb=" CA LEU F 140 " pdb=" C LEU F 140 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.30e-02 5.92e+03 5.66e+00 ... (remaining 14145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 18921 2.06 - 4.11: 452 4.11 - 6.17: 28 6.17 - 8.22: 3 8.22 - 10.28: 1 Bond angle restraints: 19405 Sorted by residual: angle pdb=" N LEU I 140 " pdb=" CA LEU I 140 " pdb=" C LEU I 140 " ideal model delta sigma weight residual 109.96 99.68 10.28 1.49e+00 4.50e-01 4.76e+01 angle pdb=" N GLY I 123 " pdb=" CA GLY I 123 " pdb=" C GLY I 123 " ideal model delta sigma weight residual 115.08 108.54 6.54 1.19e+00 7.06e-01 3.02e+01 angle pdb=" N ALA H 137 " pdb=" CA ALA H 137 " pdb=" C ALA H 137 " ideal model delta sigma weight residual 110.24 117.80 -7.56 1.46e+00 4.69e-01 2.68e+01 angle pdb=" N ALA H 147 " pdb=" CA ALA H 147 " pdb=" C ALA H 147 " ideal model delta sigma weight residual 112.24 106.25 5.99 1.28e+00 6.10e-01 2.19e+01 angle pdb=" N THR H 142 " pdb=" CA THR H 142 " pdb=" C THR H 142 " ideal model delta sigma weight residual 113.20 107.62 5.58 1.21e+00 6.83e-01 2.13e+01 ... (remaining 19400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7543 17.94 - 35.87: 630 35.87 - 53.81: 115 53.81 - 71.75: 15 71.75 - 89.68: 12 Dihedral angle restraints: 8315 sinusoidal: 3239 harmonic: 5076 Sorted by residual: dihedral pdb=" CB CYS L 61 " pdb=" SG CYS L 61 " pdb=" SG CYS K 61 " pdb=" CB CYS K 61 " ideal model delta sinusoidal sigma weight residual -86.00 -154.42 68.42 1 1.00e+01 1.00e-02 6.07e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS C 61 " pdb=" CB CYS C 61 " ideal model delta sinusoidal sigma weight residual -86.00 -33.88 -52.12 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS J 61 " pdb=" SG CYS J 61 " pdb=" SG CYS I 61 " pdb=" CB CYS I 61 " ideal model delta sinusoidal sigma weight residual -86.00 -136.65 50.65 1 1.00e+01 1.00e-02 3.51e+01 ... (remaining 8312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1326 0.026 - 0.052: 546 0.052 - 0.079: 214 0.079 - 0.105: 97 0.105 - 0.131: 28 Chirality restraints: 2211 Sorted by residual: chirality pdb=" CA ASP K 22 " pdb=" N ASP K 22 " pdb=" C ASP K 22 " pdb=" CB ASP K 22 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE L 3 " pdb=" N ILE L 3 " pdb=" C ILE L 3 " pdb=" CB ILE L 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA PRO I 135 " pdb=" N PRO I 135 " pdb=" C PRO I 135 " pdb=" CB PRO I 135 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2208 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 21 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C SER C 21 " -0.047 2.00e-02 2.50e+03 pdb=" O SER C 21 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP C 22 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 139 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ILE L 139 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE L 139 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU L 140 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 21 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C SER G 21 " -0.038 2.00e-02 2.50e+03 pdb=" O SER G 21 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP G 22 " 0.013 2.00e-02 2.50e+03 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 103 2.50 - 3.10: 11034 3.10 - 3.70: 21447 3.70 - 4.30: 27991 4.30 - 4.90: 46413 Nonbonded interactions: 106988 Sorted by model distance: nonbonded pdb=" NZ LYS H 96 " pdb=" OD2 ASP G 64 " model vdw 1.896 3.120 nonbonded pdb=" OD1 ASP F 78 " pdb=" OG SER F 81 " model vdw 1.919 3.040 nonbonded pdb=" O GLU L 14 " pdb=" OG SER L 17 " model vdw 2.106 3.040 nonbonded pdb=" O THR E 128 " pdb=" NH2 ARG E 133 " model vdw 2.114 3.120 nonbonded pdb=" O LEU A 76 " pdb=" NH2 ARG A 82 " model vdw 2.123 3.120 ... (remaining 106983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 142) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 142) selection = chain 'G' selection = (chain 'H' and resid 1 through 142) selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = (chain 'L' and resid 1 through 142) } 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: 0.070 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.440 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.004 0.052 14154 Z= 0.211 Angle : 0.702 10.279 19413 Z= 0.410 Chirality : 0.037 0.131 2211 Planarity : 0.005 0.056 2464 Dihedral : 13.672 89.685 4999 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.82 % Favored : 96.12 % Rotamer: Outliers : 1.06 % Allowed : 0.26 % Favored : 98.68 % 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 aren not related in a simple way. whole: 1.68 (0.21), residues: 1700 helix: 1.76 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -0.33 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 82 TYR 0.018 0.001 TYR H 118 PHE 0.027 0.001 PHE H 122 TRP 0.023 0.001 TRP E 71 HIS 0.004 0.001 HIS L 47 Details of bonding type rmsd covalent geometry : bond 0.00384 (14150) covalent geometry : angle 0.69972 (19405) SS BOND : bond 0.01137 ( 4) SS BOND : angle 2.88228 ( 8) hydrogen bonds : bond 0.12712 ( 925) hydrogen bonds : angle 5.75524 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 524 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9112 (tt0) cc_final: 0.8690 (mt0) REVERT: A 12 THR cc_start: 0.8501 (p) cc_final: 0.8278 (p) REVERT: A 39 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8831 (ttm170) REVERT: A 83 ASP cc_start: 0.7174 (p0) cc_final: 0.6892 (m-30) REVERT: D 8 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 61 CYS cc_start: 0.7162 (m) cc_final: 0.6639 (m) REVERT: D 121 SER cc_start: 0.8879 (t) cc_final: 0.8623 (m) REVERT: C 7 LYS cc_start: 0.8934 (tttm) cc_final: 0.8495 (ttmm) REVERT: F 7 LYS cc_start: 0.9304 (tttp) cc_final: 0.9062 (tttp) REVERT: F 43 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 59 ILE cc_start: 0.7855 (tt) cc_final: 0.7495 (pt) REVERT: F 62 TRP cc_start: 0.8802 (t-100) cc_final: 0.8521 (t-100) REVERT: E 112 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7319 (ptp-170) REVERT: H 22 ASP cc_start: 0.6576 (t70) cc_final: 0.6219 (t70) REVERT: H 82 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7665 (mmm-85) REVERT: H 87 SER cc_start: 0.8988 (t) cc_final: 0.8441 (p) REVERT: H 125 TRP cc_start: 0.8840 (t60) cc_final: 0.8554 (t60) REVERT: G 48 CYS cc_start: 0.5637 (p) cc_final: 0.4528 (t) REVERT: G 142 THR cc_start: 0.8300 (m) cc_final: 0.7961 (p) REVERT: J 7 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8581 (ttmt) REVERT: J 88 TYR cc_start: 0.7761 (t80) cc_final: 0.7487 (t80) REVERT: J 136 ASN cc_start: 0.9092 (p0) cc_final: 0.8783 (p0) REVERT: I 7 LYS cc_start: 0.8878 (tppp) cc_final: 0.8623 (tptp) REVERT: I 18 PHE cc_start: 0.8878 (t80) cc_final: 0.8408 (t80) REVERT: I 39 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8007 (mtp85) REVERT: I 64 ASP cc_start: 0.8890 (m-30) cc_final: 0.8540 (m-30) REVERT: L 38 TYR cc_start: 0.8659 (m-80) cc_final: 0.8420 (m-10) REVERT: L 66 MET cc_start: 0.8228 (mmm) cc_final: 0.7357 (mmp) REVERT: L 96 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7933 (ttpt) REVERT: L 145 GLU cc_start: 0.6454 (tp30) cc_final: 0.6103 (tp30) REVERT: K 59 ILE cc_start: 0.8219 (mm) cc_final: 0.7860 (mm) outliers start: 16 outliers final: 5 residues processed: 527 average time/residue: 0.1047 time to fit residues: 79.1879 Evaluate side-chains 391 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 386 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain L residue 143 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 51 HIS A 104 HIS C 52 HIS G 52 HIS G 136 ASN J 52 HIS L 52 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.124986 restraints weight = 22527.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127336 restraints weight = 15298.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128897 restraints weight = 11623.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129979 restraints weight = 9546.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130617 restraints weight = 8325.085| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14154 Z= 0.173 Angle : 0.690 8.902 19413 Z= 0.351 Chirality : 0.044 0.247 2211 Planarity : 0.005 0.042 2464 Dihedral : 4.641 51.746 1876 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 3.10 % Allowed : 12.01 % Favored : 84.88 % 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 aren not related in a simple way. whole: 1.68 (0.21), residues: 1700 helix: 1.65 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 127 TYR 0.026 0.002 TYR G 38 PHE 0.029 0.002 PHE C 18 TRP 0.019 0.002 TRP E 71 HIS 0.015 0.002 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00396 (14150) covalent geometry : angle 0.68718 (19405) SS BOND : bond 0.01477 ( 4) SS BOND : angle 3.17590 ( 8) hydrogen bonds : bond 0.04632 ( 925) hydrogen bonds : angle 4.59490 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 436 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9041 (tt0) cc_final: 0.8408 (tt0) REVERT: A 87 SER cc_start: 0.8870 (m) cc_final: 0.8521 (p) REVERT: A 88 TYR cc_start: 0.7961 (t80) cc_final: 0.7559 (t80) REVERT: D 8 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8021 (tm-30) REVERT: D 61 CYS cc_start: 0.6668 (m) cc_final: 0.6182 (m) REVERT: D 95 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8583 (pp) REVERT: D 99 GLN cc_start: 0.7991 (tt0) cc_final: 0.7687 (pt0) REVERT: C 7 LYS cc_start: 0.9159 (tttm) cc_final: 0.8504 (ttmm) REVERT: C 9 PHE cc_start: 0.8050 (m-80) cc_final: 0.7794 (m-10) REVERT: C 48 CYS cc_start: 0.8481 (p) cc_final: 0.7806 (m) REVERT: F 7 LYS cc_start: 0.9225 (tttp) cc_final: 0.9015 (tttp) REVERT: F 96 LYS cc_start: 0.8496 (ttpp) cc_final: 0.7941 (tmmt) REVERT: E 117 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8147 (mm-30) REVERT: H 8 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6839 (tm-30) REVERT: H 22 ASP cc_start: 0.6767 (t70) cc_final: 0.6494 (t70) REVERT: H 82 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7577 (mmm-85) REVERT: H 125 TRP cc_start: 0.9009 (t60) cc_final: 0.8785 (t60) REVERT: G 9 PHE cc_start: 0.8246 (m-80) cc_final: 0.8026 (m-10) REVERT: G 14 GLU cc_start: 0.7522 (pt0) cc_final: 0.7308 (pt0) REVERT: G 17 SER cc_start: 0.9388 (p) cc_final: 0.9009 (t) REVERT: G 40 ASP cc_start: 0.8223 (m-30) cc_final: 0.7909 (m-30) REVERT: G 78 ASP cc_start: 0.7489 (t0) cc_final: 0.7052 (t0) REVERT: J 8 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7817 (tm-30) REVERT: J 136 ASN cc_start: 0.8929 (p0) cc_final: 0.8676 (p0) REVERT: I 1 MET cc_start: 0.6152 (tpp) cc_final: 0.5921 (tpp) REVERT: I 7 LYS cc_start: 0.9010 (tppp) cc_final: 0.8713 (tptp) REVERT: I 64 ASP cc_start: 0.8652 (m-30) cc_final: 0.8155 (m-30) REVERT: L 66 MET cc_start: 0.8270 (mmm) cc_final: 0.7780 (tpp) REVERT: L 117 GLU cc_start: 0.7207 (tp30) cc_final: 0.6901 (tp30) REVERT: K 59 ILE cc_start: 0.8364 (mm) cc_final: 0.8161 (mm) REVERT: K 88 TYR cc_start: 0.8987 (t80) cc_final: 0.8584 (t80) REVERT: K 99 GLN cc_start: 0.7486 (mt0) cc_final: 0.7239 (mt0) REVERT: K 112 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7735 (ttm-80) REVERT: K 117 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7975 (mp0) outliers start: 47 outliers final: 33 residues processed: 458 average time/residue: 0.1068 time to fit residues: 70.1591 Evaluate side-chains 414 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 379 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 47 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 122 PHE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 141 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 13 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.113209 restraints weight = 22743.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115270 restraints weight = 16133.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116710 restraints weight = 12597.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117629 restraints weight = 10555.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118136 restraints weight = 9348.281| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14154 Z= 0.219 Angle : 0.706 9.176 19413 Z= 0.365 Chirality : 0.046 0.221 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.505 42.828 1871 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.24 % Rotamer: Outliers : 5.08 % Allowed : 15.78 % Favored : 79.14 % 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 aren not related in a simple way. whole: 1.52 (0.21), residues: 1700 helix: 1.47 (0.15), residues: 1189 sheet: None (None), residues: 0 loop : 0.07 (0.31), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 127 TYR 0.015 0.002 TYR B 118 PHE 0.027 0.002 PHE K 110 TRP 0.014 0.002 TRP H 102 HIS 0.040 0.002 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00522 (14150) covalent geometry : angle 0.70461 (19405) SS BOND : bond 0.00746 ( 4) SS BOND : angle 2.52831 ( 8) hydrogen bonds : bond 0.04956 ( 925) hydrogen bonds : angle 4.53467 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 418 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: B 38 TYR cc_start: 0.8937 (m-10) cc_final: 0.8735 (m-10) REVERT: B 99 GLN cc_start: 0.9119 (tt0) cc_final: 0.8670 (tt0) REVERT: B 107 CYS cc_start: 0.8545 (t) cc_final: 0.8338 (t) REVERT: B 117 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7545 (mm-30) REVERT: A 14 GLU cc_start: 0.8106 (pm20) cc_final: 0.7885 (pm20) REVERT: A 87 SER cc_start: 0.8858 (m) cc_final: 0.8518 (p) REVERT: A 88 TYR cc_start: 0.8260 (t80) cc_final: 0.7960 (t80) REVERT: D 99 GLN cc_start: 0.8139 (tt0) cc_final: 0.7805 (pt0) REVERT: C 7 LYS cc_start: 0.9166 (tttm) cc_final: 0.8751 (tttp) REVERT: C 48 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7864 (m) REVERT: F 7 LYS cc_start: 0.9329 (tttp) cc_final: 0.9122 (tttp) REVERT: F 57 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8143 (mm-40) REVERT: F 59 ILE cc_start: 0.8317 (pt) cc_final: 0.8001 (mt) REVERT: F 126 ILE cc_start: 0.9526 (tp) cc_final: 0.9296 (tp) REVERT: F 127 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7678 (mtt180) REVERT: E 3 ILE cc_start: 0.9446 (mm) cc_final: 0.8240 (tt) REVERT: E 99 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: H 60 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8775 (mm) REVERT: H 82 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7673 (mmm-85) REVERT: G 78 ASP cc_start: 0.7688 (t0) cc_final: 0.7160 (t0) REVERT: G 90 ASN cc_start: 0.8664 (m110) cc_final: 0.8455 (m110) REVERT: G 121 SER cc_start: 0.8838 (t) cc_final: 0.8273 (p) REVERT: J 136 ASN cc_start: 0.8983 (p0) cc_final: 0.8672 (p0) REVERT: J 141 SER cc_start: 0.9601 (m) cc_final: 0.9038 (p) REVERT: I 117 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8179 (mm-30) REVERT: I 136 ASN cc_start: 0.8210 (p0) cc_final: 0.7906 (p0) REVERT: L 117 GLU cc_start: 0.7254 (tp30) cc_final: 0.6956 (tp30) REVERT: L 119 LEU cc_start: 0.9206 (mt) cc_final: 0.8998 (mt) REVERT: L 145 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6563 (mm-30) REVERT: K 88 TYR cc_start: 0.9090 (t80) cc_final: 0.8796 (t80) REVERT: K 117 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7977 (mp0) outliers start: 77 outliers final: 62 residues processed: 451 average time/residue: 0.1056 time to fit residues: 68.8046 Evaluate side-chains 456 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 390 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 4 ASP Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 96 LYS Chi-restraints excluded: chain K residue 105 ILE Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 141 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 116 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 HIS G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.102793 restraints weight = 23227.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.104944 restraints weight = 16004.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.106522 restraints weight = 12363.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107531 restraints weight = 10290.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.108121 restraints weight = 9042.284| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14154 Z= 0.134 Angle : 0.644 11.924 19413 Z= 0.323 Chirality : 0.042 0.238 2211 Planarity : 0.005 0.070 2464 Dihedral : 4.298 44.218 1871 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 3.17 % Allowed : 20.40 % Favored : 76.44 % 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 aren not related in a simple way. whole: 1.70 (0.21), residues: 1700 helix: 1.63 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : 0.07 (0.31), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 28 TYR 0.019 0.001 TYR E 88 PHE 0.017 0.001 PHE C 18 TRP 0.013 0.002 TRP D 71 HIS 0.010 0.001 HIS A 47 Details of bonding type rmsd covalent geometry : bond 0.00295 (14150) covalent geometry : angle 0.64331 (19405) SS BOND : bond 0.00652 ( 4) SS BOND : angle 1.45361 ( 8) hydrogen bonds : bond 0.04239 ( 925) hydrogen bonds : angle 4.32719 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 411 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8183 (ttmm) REVERT: B 99 GLN cc_start: 0.9163 (tt0) cc_final: 0.8602 (tt0) REVERT: B 107 CYS cc_start: 0.8404 (t) cc_final: 0.8158 (t) REVERT: B 117 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 14 GLU cc_start: 0.8189 (pm20) cc_final: 0.7954 (pm20) REVERT: A 87 SER cc_start: 0.8816 (m) cc_final: 0.8487 (p) REVERT: A 88 TYR cc_start: 0.8250 (t80) cc_final: 0.7968 (t80) REVERT: D 96 LYS cc_start: 0.8774 (tttm) cc_final: 0.8385 (tttm) REVERT: D 99 GLN cc_start: 0.8191 (tt0) cc_final: 0.7969 (pt0) REVERT: C 7 LYS cc_start: 0.9121 (tttm) cc_final: 0.8680 (tttp) REVERT: C 48 CYS cc_start: 0.8373 (p) cc_final: 0.7634 (m) REVERT: C 119 LEU cc_start: 0.8963 (tt) cc_final: 0.8750 (tt) REVERT: F 7 LYS cc_start: 0.9316 (tttp) cc_final: 0.9110 (tttp) REVERT: F 43 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8050 (mm-30) REVERT: F 59 ILE cc_start: 0.8311 (pt) cc_final: 0.7946 (mt) REVERT: F 126 ILE cc_start: 0.9519 (tp) cc_final: 0.9290 (tp) REVERT: F 145 GLU cc_start: 0.6289 (tp30) cc_final: 0.5866 (tp30) REVERT: E 3 ILE cc_start: 0.9440 (mm) cc_final: 0.8211 (tt) REVERT: E 99 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8545 (mt0) REVERT: H 82 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7496 (mmm-85) REVERT: G 14 GLU cc_start: 0.7918 (pt0) cc_final: 0.7583 (pt0) REVERT: G 78 ASP cc_start: 0.7770 (t0) cc_final: 0.6365 (t0) REVERT: G 121 SER cc_start: 0.8802 (t) cc_final: 0.8263 (p) REVERT: J 66 MET cc_start: 0.8699 (mmp) cc_final: 0.8478 (mmm) REVERT: J 82 ARG cc_start: 0.5842 (mtm-85) cc_final: 0.5597 (mtt180) REVERT: J 136 ASN cc_start: 0.8907 (p0) cc_final: 0.8707 (p0) REVERT: J 141 SER cc_start: 0.9597 (m) cc_final: 0.8974 (p) REVERT: I 7 LYS cc_start: 0.8935 (tppt) cc_final: 0.8271 (tptp) REVERT: I 57 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: I 107 CYS cc_start: 0.8983 (m) cc_final: 0.8347 (t) REVERT: I 117 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8112 (mm-30) REVERT: L 117 GLU cc_start: 0.7200 (tp30) cc_final: 0.6830 (tp30) REVERT: K 32 ASP cc_start: 0.7830 (t0) cc_final: 0.7550 (t0) REVERT: K 86 VAL cc_start: 0.8655 (t) cc_final: 0.8407 (p) REVERT: K 88 TYR cc_start: 0.9080 (t80) cc_final: 0.8761 (t80) REVERT: K 108 LEU cc_start: 0.8924 (tt) cc_final: 0.8552 (tp) REVERT: K 117 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7935 (mp0) outliers start: 48 outliers final: 27 residues processed: 431 average time/residue: 0.1037 time to fit residues: 64.0780 Evaluate side-chains 421 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 391 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 118 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 97 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100274 restraints weight = 23596.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.102198 restraints weight = 17107.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103496 restraints weight = 13654.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104367 restraints weight = 11599.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.105051 restraints weight = 10424.833| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14154 Z= 0.155 Angle : 0.645 11.225 19413 Z= 0.325 Chirality : 0.043 0.237 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.240 44.083 1871 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 4.42 % Allowed : 21.45 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.21), residues: 1700 helix: 1.57 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : 0.13 (0.31), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 28 TYR 0.021 0.002 TYR L 38 PHE 0.018 0.001 PHE C 18 TRP 0.013 0.002 TRP C 62 HIS 0.006 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00363 (14150) covalent geometry : angle 0.64411 (19405) SS BOND : bond 0.00873 ( 4) SS BOND : angle 1.58448 ( 8) hydrogen bonds : bond 0.04237 ( 925) hydrogen bonds : angle 4.30765 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 415 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 8 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 28 ARG cc_start: 0.7187 (tpp-160) cc_final: 0.6155 (tpm170) REVERT: B 31 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 96 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8225 (ttmm) REVERT: B 99 GLN cc_start: 0.9122 (tt0) cc_final: 0.8661 (tt0) REVERT: B 107 CYS cc_start: 0.8511 (t) cc_final: 0.8248 (t) REVERT: B 117 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7547 (mm-30) REVERT: A 14 GLU cc_start: 0.8400 (pm20) cc_final: 0.8182 (pm20) REVERT: A 62 TRP cc_start: 0.8056 (t-100) cc_final: 0.7504 (t-100) REVERT: A 87 SER cc_start: 0.8799 (m) cc_final: 0.8500 (p) REVERT: A 88 TYR cc_start: 0.8307 (t80) cc_final: 0.8065 (t80) REVERT: D 46 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7912 (mm-30) REVERT: D 61 CYS cc_start: 0.7045 (m) cc_final: 0.6639 (m) REVERT: D 96 LYS cc_start: 0.8916 (tttm) cc_final: 0.8676 (tttt) REVERT: D 99 GLN cc_start: 0.8222 (tt0) cc_final: 0.7986 (pt0) REVERT: D 106 SER cc_start: 0.9268 (m) cc_final: 0.8890 (t) REVERT: C 55 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7915 (tt) REVERT: F 7 LYS cc_start: 0.9315 (tttp) cc_final: 0.9102 (tttp) REVERT: F 43 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8032 (mm-30) REVERT: F 59 ILE cc_start: 0.8271 (pt) cc_final: 0.7976 (mt) REVERT: F 126 ILE cc_start: 0.9533 (tp) cc_final: 0.9304 (tp) REVERT: F 145 GLU cc_start: 0.6274 (tp30) cc_final: 0.5846 (tp30) REVERT: E 3 ILE cc_start: 0.9468 (mm) cc_final: 0.8262 (tt) REVERT: E 28 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7872 (tpp-160) REVERT: E 37 LEU cc_start: 0.8960 (tp) cc_final: 0.8516 (tp) REVERT: E 43 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7988 (mm-30) REVERT: E 99 GLN cc_start: 0.8860 (mt0) cc_final: 0.8565 (mt0) REVERT: G 14 GLU cc_start: 0.7905 (pt0) cc_final: 0.7678 (pt0) REVERT: G 78 ASP cc_start: 0.8048 (t0) cc_final: 0.7350 (t0) REVERT: G 121 SER cc_start: 0.8804 (t) cc_final: 0.8273 (p) REVERT: J 136 ASN cc_start: 0.8923 (p0) cc_final: 0.8707 (p0) REVERT: J 141 SER cc_start: 0.9622 (m) cc_final: 0.9064 (p) REVERT: I 1 MET cc_start: 0.6638 (tpp) cc_final: 0.6402 (tpt) REVERT: I 57 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: I 117 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8140 (mm-30) REVERT: I 136 ASN cc_start: 0.8124 (p0) cc_final: 0.7787 (p0) REVERT: L 66 MET cc_start: 0.8346 (tpp) cc_final: 0.8096 (mpp) REVERT: L 88 TYR cc_start: 0.8594 (t80) cc_final: 0.8334 (t80) REVERT: L 117 GLU cc_start: 0.7270 (tp30) cc_final: 0.6949 (tp30) REVERT: K 32 ASP cc_start: 0.7760 (t0) cc_final: 0.7559 (t0) REVERT: K 66 MET cc_start: 0.7308 (mmp) cc_final: 0.7078 (mmp) REVERT: K 86 VAL cc_start: 0.8690 (t) cc_final: 0.8445 (p) REVERT: K 88 TYR cc_start: 0.9107 (t80) cc_final: 0.8887 (t80) REVERT: K 108 LEU cc_start: 0.8913 (tt) cc_final: 0.8573 (tp) REVERT: K 117 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: K 118 TYR cc_start: 0.8942 (t80) cc_final: 0.8661 (t80) outliers start: 67 outliers final: 47 residues processed: 449 average time/residue: 0.1014 time to fit residues: 65.5033 Evaluate side-chains 460 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 35 optimal weight: 0.0070 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.102962 restraints weight = 23238.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.105157 restraints weight = 16098.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106674 restraints weight = 12513.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107653 restraints weight = 10456.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.108231 restraints weight = 9217.276| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14154 Z= 0.123 Angle : 0.628 10.539 19413 Z= 0.310 Chirality : 0.041 0.236 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.102 45.376 1871 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.37 % Allowed : 22.90 % Favored : 73.73 % 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 aren not related in a simple way. whole: 1.80 (0.21), residues: 1700 helix: 1.64 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.26 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 39 TYR 0.020 0.001 TYR L 38 PHE 0.029 0.001 PHE K 18 TRP 0.015 0.001 TRP D 71 HIS 0.004 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00264 (14150) covalent geometry : angle 0.62790 (19405) SS BOND : bond 0.00619 ( 4) SS BOND : angle 1.31549 ( 8) hydrogen bonds : bond 0.03695 ( 925) hydrogen bonds : angle 4.19400 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 426 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 28 ARG cc_start: 0.6913 (tpp-160) cc_final: 0.6637 (tpp-160) REVERT: B 78 ASP cc_start: 0.8010 (t0) cc_final: 0.7753 (t0) REVERT: B 96 LYS cc_start: 0.8257 (ttmt) cc_final: 0.7984 (ttmm) REVERT: B 99 GLN cc_start: 0.9181 (tt0) cc_final: 0.8730 (mt0) REVERT: B 107 CYS cc_start: 0.8424 (t) cc_final: 0.8206 (t) REVERT: A 14 GLU cc_start: 0.8259 (pm20) cc_final: 0.7976 (pm20) REVERT: A 62 TRP cc_start: 0.7961 (t-100) cc_final: 0.7455 (t-100) REVERT: A 87 SER cc_start: 0.8755 (m) cc_final: 0.8481 (p) REVERT: D 26 SER cc_start: 0.8535 (t) cc_final: 0.7851 (p) REVERT: D 46 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7910 (mm-30) REVERT: D 61 CYS cc_start: 0.7117 (m) cc_final: 0.6819 (m) REVERT: D 96 LYS cc_start: 0.8831 (tttm) cc_final: 0.8567 (tttt) REVERT: D 99 GLN cc_start: 0.8123 (tt0) cc_final: 0.7919 (pt0) REVERT: D 106 SER cc_start: 0.9218 (m) cc_final: 0.8781 (t) REVERT: C 55 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7756 (tt) REVERT: F 7 LYS cc_start: 0.9370 (tttp) cc_final: 0.9154 (tttp) REVERT: F 43 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8004 (mm-30) REVERT: F 59 ILE cc_start: 0.8192 (pt) cc_final: 0.7955 (mt) REVERT: F 96 LYS cc_start: 0.8967 (tmmt) cc_final: 0.7955 (ttmt) REVERT: F 126 ILE cc_start: 0.9545 (tp) cc_final: 0.9270 (tp) REVERT: F 145 GLU cc_start: 0.5936 (tp30) cc_final: 0.5578 (tp30) REVERT: E 3 ILE cc_start: 0.9469 (mm) cc_final: 0.8285 (tt) REVERT: E 28 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7902 (tpp-160) REVERT: E 43 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8107 (mm-30) REVERT: E 99 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8520 (mt0) REVERT: H 70 THR cc_start: 0.8796 (m) cc_final: 0.8290 (t) REVERT: H 77 GLU cc_start: 0.6959 (mp0) cc_final: 0.6630 (mp0) REVERT: H 124 VAL cc_start: 0.9426 (t) cc_final: 0.9082 (p) REVERT: G 14 GLU cc_start: 0.7824 (pt0) cc_final: 0.7618 (pt0) REVERT: G 78 ASP cc_start: 0.8047 (t0) cc_final: 0.7150 (t0) REVERT: G 121 SER cc_start: 0.8782 (t) cc_final: 0.8246 (p) REVERT: J 4 ASP cc_start: 0.7851 (t70) cc_final: 0.7506 (t0) REVERT: J 141 SER cc_start: 0.9626 (m) cc_final: 0.9022 (p) REVERT: I 1 MET cc_start: 0.6458 (tpp) cc_final: 0.6217 (tpt) REVERT: I 7 LYS cc_start: 0.8964 (tppt) cc_final: 0.8325 (tptp) REVERT: I 57 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: I 107 CYS cc_start: 0.8805 (m) cc_final: 0.8289 (t) REVERT: L 39 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7622 (tpp80) REVERT: L 88 TYR cc_start: 0.8577 (t80) cc_final: 0.8304 (t80) REVERT: L 117 GLU cc_start: 0.7145 (tp30) cc_final: 0.6832 (tp30) REVERT: K 32 ASP cc_start: 0.7777 (t0) cc_final: 0.7524 (t0) REVERT: K 86 VAL cc_start: 0.8672 (t) cc_final: 0.8379 (p) REVERT: K 88 TYR cc_start: 0.8933 (t80) cc_final: 0.8674 (t80) REVERT: K 108 LEU cc_start: 0.8856 (tt) cc_final: 0.8581 (tp) REVERT: K 117 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: K 118 TYR cc_start: 0.9076 (t80) cc_final: 0.8760 (t80) outliers start: 51 outliers final: 30 residues processed: 450 average time/residue: 0.1003 time to fit residues: 65.6589 Evaluate side-chains 431 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 396 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 162 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 136 ASN J 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.095281 restraints weight = 23738.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.097011 restraints weight = 17700.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098157 restraints weight = 14311.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099039 restraints weight = 12388.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099510 restraints weight = 11179.630| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14154 Z= 0.199 Angle : 0.708 12.121 19413 Z= 0.357 Chirality : 0.045 0.218 2211 Planarity : 0.005 0.072 2464 Dihedral : 4.243 48.347 1870 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 5.02 % Allowed : 23.04 % Favored : 71.95 % 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 aren not related in a simple way. whole: 1.45 (0.21), residues: 1700 helix: 1.41 (0.15), residues: 1199 sheet: None (None), residues: 0 loop : 0.05 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 39 TYR 0.019 0.002 TYR L 38 PHE 0.027 0.002 PHE C 18 TRP 0.015 0.002 TRP C 62 HIS 0.007 0.002 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00477 (14150) covalent geometry : angle 0.70775 (19405) SS BOND : bond 0.00877 ( 4) SS BOND : angle 1.65134 ( 8) hydrogen bonds : bond 0.04712 ( 925) hydrogen bonds : angle 4.38327 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 428 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7452 (tpp-160) cc_final: 0.7229 (tpp-160) REVERT: B 31 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8675 (mt) REVERT: B 78 ASP cc_start: 0.8278 (t0) cc_final: 0.8043 (t0) REVERT: B 96 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8254 (ttmm) REVERT: B 99 GLN cc_start: 0.9140 (tt0) cc_final: 0.8661 (tt0) REVERT: B 107 CYS cc_start: 0.8591 (t) cc_final: 0.8333 (t) REVERT: A 14 GLU cc_start: 0.8391 (pm20) cc_final: 0.8163 (pm20) REVERT: A 62 TRP cc_start: 0.8198 (t-100) cc_final: 0.7526 (t-100) REVERT: A 95 LEU cc_start: 0.8528 (tt) cc_final: 0.8127 (tp) REVERT: D 46 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 61 CYS cc_start: 0.7128 (m) cc_final: 0.6797 (m) REVERT: D 106 SER cc_start: 0.9269 (m) cc_final: 0.8921 (t) REVERT: C 55 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7898 (tt) REVERT: C 60 LEU cc_start: 0.9272 (mm) cc_final: 0.9035 (mt) REVERT: C 75 ASN cc_start: 0.7041 (m-40) cc_final: 0.6669 (t0) REVERT: F 29 ASP cc_start: 0.8585 (m-30) cc_final: 0.8342 (m-30) REVERT: F 43 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8048 (mm-30) REVERT: F 57 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8626 (mm-40) REVERT: F 96 LYS cc_start: 0.9173 (tmmt) cc_final: 0.8127 (ttmt) REVERT: F 126 ILE cc_start: 0.9565 (tp) cc_final: 0.9350 (tp) REVERT: F 145 GLU cc_start: 0.5963 (tp30) cc_final: 0.5599 (tp30) REVERT: E 3 ILE cc_start: 0.9579 (mm) cc_final: 0.8407 (tt) REVERT: E 28 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (tpp-160) REVERT: E 43 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8025 (mm-30) REVERT: E 99 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: H 70 THR cc_start: 0.8911 (m) cc_final: 0.8410 (t) REVERT: H 77 GLU cc_start: 0.6920 (mp0) cc_final: 0.6710 (mp0) REVERT: G 66 MET cc_start: 0.8393 (tpp) cc_final: 0.8086 (mmp) REVERT: G 121 SER cc_start: 0.8829 (t) cc_final: 0.8306 (p) REVERT: J 125 TRP cc_start: 0.9408 (t60) cc_final: 0.8653 (t60) REVERT: J 141 SER cc_start: 0.9638 (m) cc_final: 0.9140 (p) REVERT: I 57 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: I 136 ASN cc_start: 0.8308 (p0) cc_final: 0.7996 (p0) REVERT: L 66 MET cc_start: 0.8309 (tpp) cc_final: 0.7866 (tpp) REVERT: L 117 GLU cc_start: 0.7377 (tp30) cc_final: 0.7101 (tp30) REVERT: K 32 ASP cc_start: 0.7846 (t0) cc_final: 0.7588 (t0) REVERT: K 86 VAL cc_start: 0.8732 (t) cc_final: 0.8478 (p) REVERT: K 108 LEU cc_start: 0.8877 (tt) cc_final: 0.8564 (tp) REVERT: K 117 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7153 (mp0) outliers start: 76 outliers final: 52 residues processed: 468 average time/residue: 0.1016 time to fit residues: 68.7852 Evaluate side-chains 470 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 412 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 164 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 126 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.094920 restraints weight = 23518.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096666 restraints weight = 17286.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.097879 restraints weight = 13934.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098693 restraints weight = 12024.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.099007 restraints weight = 10812.421| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14154 Z= 0.171 Angle : 0.689 11.544 19413 Z= 0.344 Chirality : 0.044 0.223 2211 Planarity : 0.005 0.073 2464 Dihedral : 4.232 50.002 1870 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 4.55 % Allowed : 24.16 % Favored : 71.29 % 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 aren not related in a simple way. whole: 1.57 (0.21), residues: 1700 helix: 1.50 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : 0.07 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 28 TYR 0.024 0.002 TYR A 38 PHE 0.026 0.002 PHE C 18 TRP 0.023 0.002 TRP F 62 HIS 0.005 0.001 HIS L 104 Details of bonding type rmsd covalent geometry : bond 0.00406 (14150) covalent geometry : angle 0.68855 (19405) SS BOND : bond 0.00933 ( 4) SS BOND : angle 1.50893 ( 8) hydrogen bonds : bond 0.04488 ( 925) hydrogen bonds : angle 4.27837 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 419 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7491 (tpp-160) cc_final: 0.7273 (tpp-160) REVERT: B 31 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 38 TYR cc_start: 0.8817 (m-10) cc_final: 0.8507 (m-10) REVERT: B 78 ASP cc_start: 0.8076 (t0) cc_final: 0.7870 (t0) REVERT: B 96 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8232 (ttmm) REVERT: B 99 GLN cc_start: 0.9153 (tt0) cc_final: 0.8726 (tt0) REVERT: B 107 CYS cc_start: 0.8557 (t) cc_final: 0.8273 (t) REVERT: A 14 GLU cc_start: 0.8365 (pm20) cc_final: 0.8135 (pm20) REVERT: A 23 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7031 (p90) REVERT: A 62 TRP cc_start: 0.8131 (t-100) cc_final: 0.7528 (t-100) REVERT: D 26 SER cc_start: 0.8848 (t) cc_final: 0.8356 (p) REVERT: D 46 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7819 (mm-30) REVERT: D 61 CYS cc_start: 0.7038 (m) cc_final: 0.6680 (m) REVERT: D 106 SER cc_start: 0.9197 (m) cc_final: 0.8843 (t) REVERT: C 21 SER cc_start: 0.8511 (m) cc_final: 0.7687 (p) REVERT: C 55 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7812 (tt) REVERT: C 75 ASN cc_start: 0.7181 (m-40) cc_final: 0.6701 (t0) REVERT: F 96 LYS cc_start: 0.8877 (tmmt) cc_final: 0.8147 (ttmt) REVERT: F 126 ILE cc_start: 0.9581 (tp) cc_final: 0.9373 (tp) REVERT: F 145 GLU cc_start: 0.6015 (tp30) cc_final: 0.5618 (tp30) REVERT: E 3 ILE cc_start: 0.9675 (mm) cc_final: 0.8552 (tt) REVERT: E 28 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8141 (tpp-160) REVERT: E 43 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7984 (mm-30) REVERT: E 99 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8591 (mt0) REVERT: H 70 THR cc_start: 0.8902 (m) cc_final: 0.8388 (p) REVERT: H 77 GLU cc_start: 0.6926 (mp0) cc_final: 0.6661 (mp0) REVERT: G 66 MET cc_start: 0.8392 (tpp) cc_final: 0.8061 (mmp) REVERT: G 121 SER cc_start: 0.8982 (t) cc_final: 0.8679 (t) REVERT: J 141 SER cc_start: 0.9658 (m) cc_final: 0.9137 (p) REVERT: I 1 MET cc_start: 0.6623 (tpt) cc_final: 0.6341 (mmm) REVERT: I 57 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: I 136 ASN cc_start: 0.8339 (p0) cc_final: 0.8055 (p0) REVERT: L 8 GLU cc_start: 0.8597 (pm20) cc_final: 0.7831 (pp20) REVERT: L 66 MET cc_start: 0.8341 (tpp) cc_final: 0.7846 (tpp) REVERT: L 88 TYR cc_start: 0.8812 (t80) cc_final: 0.8509 (t80) REVERT: L 117 GLU cc_start: 0.7340 (tp30) cc_final: 0.6950 (tp30) REVERT: K 86 VAL cc_start: 0.8869 (t) cc_final: 0.8626 (p) REVERT: K 108 LEU cc_start: 0.8952 (tt) cc_final: 0.8712 (tp) REVERT: K 117 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7140 (mp0) outliers start: 69 outliers final: 53 residues processed: 458 average time/residue: 0.1011 time to fit residues: 67.1012 Evaluate side-chains 466 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 109 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN F 90 ASN G 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.096081 restraints weight = 23485.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098059 restraints weight = 16702.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.099400 restraints weight = 13186.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.100270 restraints weight = 11187.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100969 restraints weight = 9989.606| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14154 Z= 0.137 Angle : 0.678 11.840 19413 Z= 0.335 Chirality : 0.042 0.231 2211 Planarity : 0.005 0.074 2464 Dihedral : 4.145 52.103 1870 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 3.76 % Allowed : 25.41 % 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 aren not related in a simple way. whole: 1.68 (0.21), residues: 1700 helix: 1.58 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.14 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 82 TYR 0.020 0.002 TYR K 88 PHE 0.019 0.001 PHE C 18 TRP 0.011 0.001 TRP H 102 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00305 (14150) covalent geometry : angle 0.67716 (19405) SS BOND : bond 0.00877 ( 4) SS BOND : angle 1.42036 ( 8) hydrogen bonds : bond 0.04062 ( 925) hydrogen bonds : angle 4.20507 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 423 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8430 (mp) REVERT: B 38 TYR cc_start: 0.8733 (m-10) cc_final: 0.8443 (m-10) REVERT: B 96 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8177 (ttmm) REVERT: B 99 GLN cc_start: 0.9236 (tt0) cc_final: 0.8737 (tt0) REVERT: B 107 CYS cc_start: 0.8520 (t) cc_final: 0.8222 (t) REVERT: A 14 GLU cc_start: 0.8390 (pm20) cc_final: 0.8020 (pm20) REVERT: A 23 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6522 (p90) REVERT: A 62 TRP cc_start: 0.8120 (t-100) cc_final: 0.7415 (t-100) REVERT: D 26 SER cc_start: 0.8747 (t) cc_final: 0.8224 (p) REVERT: D 61 CYS cc_start: 0.7115 (m) cc_final: 0.6889 (m) REVERT: D 106 SER cc_start: 0.9166 (m) cc_final: 0.8801 (t) REVERT: C 21 SER cc_start: 0.8327 (m) cc_final: 0.7518 (p) REVERT: C 39 ARG cc_start: 0.7764 (tpp80) cc_final: 0.7464 (ttm-80) REVERT: C 55 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7951 (tt) REVERT: C 75 ASN cc_start: 0.7160 (m-40) cc_final: 0.6764 (t0) REVERT: C 119 LEU cc_start: 0.9096 (tt) cc_final: 0.8828 (tt) REVERT: F 96 LYS cc_start: 0.8810 (tmmt) cc_final: 0.8078 (ttmt) REVERT: F 145 GLU cc_start: 0.5945 (tp30) cc_final: 0.5597 (tp30) REVERT: E 3 ILE cc_start: 0.9666 (mm) cc_final: 0.8454 (tt) REVERT: E 28 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8077 (tpp-160) REVERT: E 43 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7977 (mm-30) REVERT: E 99 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (mt0) REVERT: E 118 TYR cc_start: 0.9245 (t80) cc_final: 0.9042 (t80) REVERT: H 70 THR cc_start: 0.8728 (m) cc_final: 0.8473 (t) REVERT: H 77 GLU cc_start: 0.6463 (mp0) cc_final: 0.6078 (mp0) REVERT: H 121 SER cc_start: 0.9478 (m) cc_final: 0.9095 (t) REVERT: H 124 VAL cc_start: 0.9432 (t) cc_final: 0.9153 (p) REVERT: G 66 MET cc_start: 0.8702 (tpp) cc_final: 0.8327 (mmp) REVERT: G 121 SER cc_start: 0.8953 (t) cc_final: 0.8649 (t) REVERT: J 141 SER cc_start: 0.9674 (m) cc_final: 0.9155 (p) REVERT: I 1 MET cc_start: 0.6558 (tpt) cc_final: 0.6241 (tpt) REVERT: I 28 ARG cc_start: 0.8292 (mmm160) cc_final: 0.8016 (mmm160) REVERT: I 57 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: I 136 ASN cc_start: 0.8255 (p0) cc_final: 0.7963 (p0) REVERT: L 8 GLU cc_start: 0.8569 (pm20) cc_final: 0.7740 (pp20) REVERT: L 39 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7819 (tpp80) REVERT: L 88 TYR cc_start: 0.8756 (t80) cc_final: 0.8496 (t80) REVERT: L 117 GLU cc_start: 0.7230 (tp30) cc_final: 0.6830 (tp30) REVERT: K 86 VAL cc_start: 0.8862 (t) cc_final: 0.8609 (p) REVERT: K 117 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7113 (mp0) outliers start: 57 outliers final: 44 residues processed: 454 average time/residue: 0.1006 time to fit residues: 66.5864 Evaluate side-chains 464 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 413 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 102 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN G 136 ASN J 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.097617 restraints weight = 23307.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099463 restraints weight = 16970.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100707 restraints weight = 13582.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.101607 restraints weight = 11593.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102085 restraints weight = 10397.104| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14154 Z= 0.137 Angle : 0.689 11.861 19413 Z= 0.338 Chirality : 0.042 0.238 2211 Planarity : 0.005 0.074 2464 Dihedral : 4.094 54.258 1870 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.37 % Allowed : 26.07 % Favored : 70.56 % 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 aren not related in a simple way. whole: 1.71 (0.21), residues: 1700 helix: 1.58 (0.15), residues: 1198 sheet: None (None), residues: 0 loop : 0.20 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 82 TYR 0.021 0.002 TYR K 88 PHE 0.029 0.001 PHE K 18 TRP 0.013 0.001 TRP C 71 HIS 0.004 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00309 (14150) covalent geometry : angle 0.68842 (19405) SS BOND : bond 0.00864 ( 4) SS BOND : angle 1.40762 ( 8) hydrogen bonds : bond 0.03881 ( 925) hydrogen bonds : angle 4.16977 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 423 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8397 (mp) REVERT: B 38 TYR cc_start: 0.8712 (m-10) cc_final: 0.8396 (m-10) REVERT: B 96 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8150 (ttmm) REVERT: B 99 GLN cc_start: 0.9254 (tt0) cc_final: 0.8699 (tt0) REVERT: B 107 CYS cc_start: 0.8504 (t) cc_final: 0.8219 (t) REVERT: A 14 GLU cc_start: 0.8421 (pm20) cc_final: 0.8136 (pm20) REVERT: A 23 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6474 (p90) REVERT: A 62 TRP cc_start: 0.8100 (t-100) cc_final: 0.7427 (t-100) REVERT: D 26 SER cc_start: 0.8719 (t) cc_final: 0.8198 (p) REVERT: D 61 CYS cc_start: 0.7116 (m) cc_final: 0.6881 (m) REVERT: D 106 SER cc_start: 0.9155 (m) cc_final: 0.8780 (t) REVERT: C 21 SER cc_start: 0.8337 (m) cc_final: 0.7664 (p) REVERT: C 39 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7448 (ttm-80) REVERT: C 55 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7917 (tt) REVERT: C 75 ASN cc_start: 0.7163 (m-40) cc_final: 0.6607 (m110) REVERT: F 66 MET cc_start: 0.7826 (mmm) cc_final: 0.7604 (tpp) REVERT: F 96 LYS cc_start: 0.8802 (tmmt) cc_final: 0.8077 (ttmt) REVERT: E 3 ILE cc_start: 0.9666 (mm) cc_final: 0.8463 (tt) REVERT: E 28 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8059 (tpp-160) REVERT: E 43 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7920 (mm-30) REVERT: E 64 ASP cc_start: 0.8047 (m-30) cc_final: 0.7808 (m-30) REVERT: E 99 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8566 (mt0) REVERT: E 118 TYR cc_start: 0.9274 (t80) cc_final: 0.9016 (t80) REVERT: H 70 THR cc_start: 0.8685 (m) cc_final: 0.8451 (t) REVERT: H 77 GLU cc_start: 0.6436 (mp0) cc_final: 0.6087 (mp0) REVERT: H 121 SER cc_start: 0.9470 (m) cc_final: 0.9086 (t) REVERT: H 124 VAL cc_start: 0.9447 (t) cc_final: 0.9157 (p) REVERT: G 43 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: G 46 GLU cc_start: 0.7889 (mp0) cc_final: 0.7632 (mp0) REVERT: G 66 MET cc_start: 0.8713 (tpp) cc_final: 0.8346 (mmp) REVERT: G 121 SER cc_start: 0.8972 (t) cc_final: 0.8670 (t) REVERT: J 141 SER cc_start: 0.9671 (m) cc_final: 0.9145 (p) REVERT: I 1 MET cc_start: 0.6544 (tpt) cc_final: 0.6211 (tpt) REVERT: I 28 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7914 (mmm160) REVERT: I 29 ASP cc_start: 0.8275 (m-30) cc_final: 0.7458 (t0) REVERT: I 57 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: I 136 ASN cc_start: 0.8217 (p0) cc_final: 0.7931 (p0) REVERT: L 8 GLU cc_start: 0.8667 (pm20) cc_final: 0.7890 (pp20) REVERT: L 39 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7714 (tpp80) REVERT: L 88 TYR cc_start: 0.8730 (t80) cc_final: 0.8468 (t80) REVERT: L 117 GLU cc_start: 0.7231 (tp30) cc_final: 0.6857 (tp30) REVERT: K 86 VAL cc_start: 0.8846 (t) cc_final: 0.8610 (p) REVERT: K 117 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7154 (mp0) outliers start: 51 outliers final: 38 residues processed: 452 average time/residue: 0.0976 time to fit residues: 64.2988 Evaluate side-chains 453 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 407 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 23 PHE Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 28 ARG Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 47 HIS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 43 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 50 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS F 90 ASN G 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.098061 restraints weight = 23516.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.100110 restraints weight = 16634.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.101507 restraints weight = 13073.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102463 restraints weight = 11020.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.103044 restraints weight = 9779.419| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14154 Z= 0.134 Angle : 0.686 11.849 19413 Z= 0.337 Chirality : 0.042 0.234 2211 Planarity : 0.005 0.074 2464 Dihedral : 4.054 58.604 1870 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 3.10 % Allowed : 26.86 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.21), residues: 1700 helix: 1.55 (0.15), residues: 1209 sheet: None (None), residues: 0 loop : 0.13 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 127 TYR 0.020 0.001 TYR K 88 PHE 0.024 0.001 PHE E 18 TRP 0.018 0.001 TRP F 71 HIS 0.004 0.001 HIS G 104 Details of bonding type rmsd covalent geometry : bond 0.00301 (14150) covalent geometry : angle 0.68512 (19405) SS BOND : bond 0.00830 ( 4) SS BOND : angle 1.36816 ( 8) hydrogen bonds : bond 0.03688 ( 925) hydrogen bonds : angle 4.16891 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2004.56 seconds wall clock time: 35 minutes 25.44 seconds (2125.44 seconds total)