Starting phenix.real_space_refine on Thu May 15 16:18:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghs_40049/05_2025/8ghs_40049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghs_40049/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghs_40049/05_2025/8ghs_40049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghs_40049/05_2025/8ghs_40049.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghs_40049/05_2025/8ghs_40049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghs_40049/05_2025/8ghs_40049.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.23, per 1000 atoms: 0.60 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: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.08 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: 3.55 Time building geometry restraints manager: 3.89 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: 0.130 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.380 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (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 TRP 0.023 0.001 TRP E 71 HIS 0.004 0.001 HIS L 47 PHE 0.027 0.001 PHE H 122 TYR 0.018 0.001 TYR H 118 ARG 0.010 0.001 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.12712 ( 925) hydrogen bonds : angle 5.75524 ( 2712) SS BOND : bond 0.01137 ( 4) SS BOND : angle 2.88228 ( 8) covalent geometry : bond 0.00384 (14150) covalent geometry : angle 0.69972 (19405) *********************** 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 : 1.358 Fit side-chains revert: symmetry clash REVERT: B 99 GLN cc_start: 0.9112 (tt0) cc_final: 0.8689 (mt0) REVERT: A 12 THR cc_start: 0.8501 (p) cc_final: 0.8277 (p) REVERT: A 39 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8832 (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: 0.6640 (m) REVERT: D 121 SER cc_start: 0.8879 (t) cc_final: 0.8624 (m) REVERT: C 7 LYS cc_start: 0.8934 (tttm) cc_final: 0.8494 (ttmm) REVERT: F 7 LYS cc_start: 0.9304 (tttp) cc_final: 0.9063 (tttp) REVERT: F 59 ILE cc_start: 0.7855 (tt) cc_final: 0.7466 (pt) REVERT: F 62 TRP cc_start: 0.8802 (t-100) cc_final: 0.8515 (t-100) REVERT: E 112 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7321 (ptp-170) REVERT: H 22 ASP cc_start: 0.6576 (t70) cc_final: 0.6220 (t70) REVERT: H 82 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7664 (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: 0.4529 (t) REVERT: G 142 THR cc_start: 0.8300 (m) cc_final: 0.7962 (p) REVERT: J 7 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8584 (ttmt) REVERT: J 88 TYR cc_start: 0.7761 (t80) cc_final: 0.7484 (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: 0.8626 (tptp) REVERT: I 18 PHE cc_start: 0.8878 (t80) cc_final: 0.8405 (t80) REVERT: I 39 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8008 (mtp85) REVERT: I 64 ASP cc_start: 0.8890 (m-30) cc_final: 0.8536 (m-30) REVERT: L 38 TYR cc_start: 0.8659 (m-80) cc_final: 0.8421 (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: 0.6104 (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: 0.2519 time to fit residues: 188.9220 Evaluate side-chains 390 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 385 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 142 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 104 HIS C 52 HIS G 52 HIS G 136 ASN J 52 HIS J 57 GLN L 52 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129740 restraints weight = 22139.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132044 restraints weight = 15102.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133605 restraints weight = 11495.124| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14154 Z= 0.159 Angle : 0.695 9.603 19413 Z= 0.349 Chirality : 0.043 0.272 2211 Planarity : 0.005 0.041 2464 Dihedral : 4.627 52.001 1876 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.64 % Allowed : 12.08 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1700 helix: 1.67 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : 0.01 (0.30), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 71 HIS 0.016 0.001 HIS A 47 PHE 0.027 0.002 PHE C 18 TYR 0.027 0.002 TYR G 38 ARG 0.007 0.001 ARG F 127 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 925) hydrogen bonds : angle 4.56767 ( 2712) SS BOND : bond 0.00897 ( 4) SS BOND : angle 2.38852 ( 8) covalent geometry : bond 0.00354 (14150) covalent geometry : angle 0.69314 (19405) *********************** 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 468 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ASP cc_start: 0.7863 (t0) cc_final: 0.6245 (m-30) REVERT: B 99 GLN cc_start: 0.9017 (tt0) cc_final: 0.8376 (tt0) REVERT: A 87 SER cc_start: 0.8863 (m) cc_final: 0.8514 (p) REVERT: A 88 TYR cc_start: 0.7938 (t80) cc_final: 0.7513 (t80) REVERT: D 8 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 61 CYS cc_start: 0.6634 (m) cc_final: 0.6178 (m) REVERT: C 7 LYS cc_start: 0.9167 (tttm) cc_final: 0.8505 (ttmm) REVERT: C 9 PHE cc_start: 0.7917 (m-80) cc_final: 0.7634 (m-10) REVERT: F 7 LYS cc_start: 0.9170 (tttp) cc_final: 0.8925 (tttp) REVERT: F 19 LEU cc_start: 0.9289 (mt) cc_final: 0.9056 (mt) REVERT: F 96 LYS cc_start: 0.8447 (ttpp) cc_final: 0.7923 (tmmt) REVERT: E 112 ARG cc_start: 0.7579 (ttm110) cc_final: 0.7370 (ttm110) REVERT: E 117 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8166 (mm-30) REVERT: H 8 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6621 (tm-30) REVERT: H 22 ASP cc_start: 0.6669 (t70) cc_final: 0.6411 (t70) REVERT: H 82 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7519 (mmm-85) REVERT: H 125 TRP cc_start: 0.9016 (t60) cc_final: 0.8797 (t60) REVERT: G 14 GLU cc_start: 0.7525 (pt0) cc_final: 0.7306 (pt0) REVERT: G 17 SER cc_start: 0.9380 (p) cc_final: 0.8994 (t) REVERT: G 40 ASP cc_start: 0.8211 (m-30) cc_final: 0.7928 (m-30) REVERT: G 78 ASP cc_start: 0.7444 (t0) cc_final: 0.6449 (t0) REVERT: J 8 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7826 (tm-30) REVERT: J 136 ASN cc_start: 0.8907 (p0) cc_final: 0.8697 (p0) REVERT: I 7 LYS cc_start: 0.8988 (tppp) cc_final: 0.8688 (tptp) REVERT: I 64 ASP cc_start: 0.8636 (m-30) cc_final: 0.8168 (m-30) REVERT: L 66 MET cc_start: 0.8254 (mmm) cc_final: 0.7962 (tpp) REVERT: K 59 ILE cc_start: 0.8322 (mm) cc_final: 0.8101 (mm) REVERT: K 66 MET cc_start: 0.7239 (mmp) cc_final: 0.6790 (mmt) REVERT: K 88 TYR cc_start: 0.8917 (t80) cc_final: 0.8537 (t80) REVERT: K 112 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7637 (ttm-80) REVERT: K 117 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6950 (mp0) outliers start: 40 outliers final: 25 residues processed: 444 average time/residue: 0.2544 time to fit residues: 161.3442 Evaluate side-chains 404 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 378 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 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 141 SER 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 61 CYS Chi-restraints excluded: chain E residue 87 SER 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 89 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain K residue 117 GLU 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 48 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 134 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** 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 = 0.3399 r_free = 0.3399 target = 0.125498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107499 restraints weight = 23018.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109653 restraints weight = 16092.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110977 restraints weight = 12520.214| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14154 Z= 0.168 Angle : 0.660 10.301 19413 Z= 0.336 Chirality : 0.044 0.240 2211 Planarity : 0.005 0.069 2464 Dihedral : 4.291 43.125 1871 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 4.03 % Allowed : 15.38 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.21), residues: 1700 helix: 1.62 (0.15), residues: 1189 sheet: None (None), residues: 0 loop : 0.17 (0.31), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 71 HIS 0.009 0.002 HIS A 47 PHE 0.024 0.002 PHE K 110 TYR 0.021 0.002 TYR E 88 ARG 0.010 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 925) hydrogen bonds : angle 4.41504 ( 2712) SS BOND : bond 0.01156 ( 4) SS BOND : angle 2.09590 ( 8) covalent geometry : bond 0.00388 (14150) covalent geometry : angle 0.65894 (19405) *********************** 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 470 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 409 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ASP cc_start: 0.7985 (t0) cc_final: 0.7728 (t0) REVERT: B 99 GLN cc_start: 0.9145 (tt0) cc_final: 0.8615 (tt0) REVERT: A 14 GLU cc_start: 0.8171 (pm20) cc_final: 0.7897 (pm20) REVERT: A 87 SER cc_start: 0.8822 (m) cc_final: 0.8482 (p) REVERT: A 88 TYR cc_start: 0.8227 (t80) cc_final: 0.7921 (t80) REVERT: D 8 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D 61 CYS cc_start: 0.6783 (m) cc_final: 0.6357 (m) REVERT: D 96 LYS cc_start: 0.8715 (tttm) cc_final: 0.8323 (tttm) REVERT: C 7 LYS cc_start: 0.9225 (tttm) cc_final: 0.8778 (tttp) REVERT: C 48 CYS cc_start: 0.8397 (p) cc_final: 0.7617 (m) REVERT: F 59 ILE cc_start: 0.8077 (pt) cc_final: 0.7746 (mt) REVERT: F 127 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7131 (mtt180) REVERT: E 99 GLN cc_start: 0.8852 (mt0) cc_final: 0.8534 (mt0) REVERT: E 117 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8212 (mm-30) REVERT: H 55 LEU cc_start: 0.8370 (tt) cc_final: 0.8159 (tt) REVERT: H 82 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7512 (mmm-85) REVERT: G 14 GLU cc_start: 0.7906 (pt0) cc_final: 0.7443 (pt0) REVERT: G 17 SER cc_start: 0.9404 (p) cc_final: 0.9090 (t) REVERT: G 78 ASP cc_start: 0.7622 (t0) cc_final: 0.6408 (t0) REVERT: G 121 SER cc_start: 0.8785 (t) cc_final: 0.8269 (p) REVERT: J 8 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8151 (tm-30) REVERT: J 141 SER cc_start: 0.9556 (m) cc_final: 0.8952 (p) REVERT: I 7 LYS cc_start: 0.9015 (tppp) cc_final: 0.8494 (tptp) REVERT: I 14 GLU cc_start: 0.7075 (pp20) cc_final: 0.6829 (pp20) REVERT: I 117 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8087 (mm-30) REVERT: L 66 MET cc_start: 0.8477 (mmm) cc_final: 0.7885 (tpp) REVERT: L 90 ASN cc_start: 0.8562 (t0) cc_final: 0.8184 (m-40) REVERT: L 117 GLU cc_start: 0.7251 (tp30) cc_final: 0.6880 (tp30) REVERT: K 117 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7942 (mp0) outliers start: 61 outliers final: 44 residues processed: 436 average time/residue: 0.2506 time to fit residues: 156.4194 Evaluate side-chains 424 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 379 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 142 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 124 VAL 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 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 87 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 74 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 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain L residue 16 LEU 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 117 GLU Chi-restraints excluded: chain K residue 119 LEU 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 2 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN I 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.117135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.099291 restraints weight = 23335.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100912 restraints weight = 17226.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102261 restraints weight = 14029.054| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 14154 Z= 0.202 Angle : 0.690 11.518 19413 Z= 0.354 Chirality : 0.046 0.232 2211 Planarity : 0.005 0.045 2464 Dihedral : 4.438 44.500 1871 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 4.95 % Allowed : 18.88 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1700 helix: 1.49 (0.15), residues: 1183 sheet: None (None), residues: 0 loop : 0.04 (0.31), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 71 HIS 0.007 0.002 HIS B 51 PHE 0.023 0.002 PHE C 18 TYR 0.018 0.002 TYR L 38 ARG 0.005 0.001 ARG F 127 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 925) hydrogen bonds : angle 4.39889 ( 2712) SS BOND : bond 0.01004 ( 4) SS BOND : angle 1.77908 ( 8) covalent geometry : bond 0.00483 (14150) covalent geometry : angle 0.68900 (19405) *********************** 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 503 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 428 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8726 (mt) REVERT: B 78 ASP cc_start: 0.8159 (t0) cc_final: 0.7711 (t0) REVERT: B 99 GLN cc_start: 0.9163 (tt0) cc_final: 0.8647 (tt0) REVERT: A 14 GLU cc_start: 0.8246 (pm20) cc_final: 0.7951 (pm20) REVERT: A 87 SER cc_start: 0.8776 (m) cc_final: 0.8511 (p) REVERT: D 60 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9147 (mm) REVERT: C 7 LYS cc_start: 0.9182 (tttm) cc_final: 0.8786 (tttp) REVERT: F 117 GLU cc_start: 0.4584 (tm-30) cc_final: 0.4186 (tm-30) REVERT: F 126 ILE cc_start: 0.9512 (tp) cc_final: 0.9302 (tp) REVERT: E 3 ILE cc_start: 0.9488 (mm) cc_final: 0.8368 (tt) REVERT: E 43 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8041 (mm-30) REVERT: E 99 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: H 8 GLU cc_start: 0.7346 (tm-30) cc_final: 0.7065 (tm-30) REVERT: H 60 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8642 (mm) REVERT: H 70 THR cc_start: 0.9008 (m) cc_final: 0.8473 (p) REVERT: H 82 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7870 (mtm-85) REVERT: H 99 GLN cc_start: 0.8576 (tt0) cc_final: 0.8372 (tt0) REVERT: G 9 PHE cc_start: 0.8612 (m-10) cc_final: 0.8211 (m-10) REVERT: G 14 GLU cc_start: 0.7953 (pt0) cc_final: 0.7719 (pt0) REVERT: G 39 ARG cc_start: 0.8296 (ttp-170) cc_final: 0.7887 (ttp-170) REVERT: G 40 ASP cc_start: 0.8344 (m-30) cc_final: 0.8072 (m-30) REVERT: G 78 ASP cc_start: 0.8056 (t0) cc_final: 0.7292 (t0) REVERT: G 107 CYS cc_start: 0.9016 (m) cc_final: 0.8718 (m) REVERT: G 121 SER cc_start: 0.8826 (t) cc_final: 0.8283 (p) REVERT: J 8 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8391 (tm-30) REVERT: J 125 TRP cc_start: 0.9459 (t60) cc_final: 0.8729 (t60) REVERT: J 136 ASN cc_start: 0.9077 (p0) cc_final: 0.8822 (p0) REVERT: J 141 SER cc_start: 0.9608 (m) cc_final: 0.9033 (p) REVERT: I 57 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: I 117 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8201 (mm-30) REVERT: I 136 ASN cc_start: 0.8244 (p0) cc_final: 0.7947 (p0) REVERT: K 6 TYR cc_start: 0.8903 (m-80) cc_final: 0.8659 (m-80) REVERT: K 70 THR cc_start: 0.8440 (m) cc_final: 0.8208 (p) REVERT: K 86 VAL cc_start: 0.8688 (t) cc_final: 0.8481 (p) REVERT: K 88 TYR cc_start: 0.9182 (t80) cc_final: 0.8856 (t80) REVERT: K 108 LEU cc_start: 0.8923 (tt) cc_final: 0.8576 (tp) REVERT: K 117 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.6948 (mp0) outliers start: 75 outliers final: 53 residues processed: 466 average time/residue: 0.2572 time to fit residues: 170.2147 Evaluate side-chains 455 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 396 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 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 59 ILE Chi-restraints excluded: chain A residue 67 THR 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 93 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE 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 12 THR 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 67 THR Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 140 LEU 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 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 142 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 26 SER 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 57 GLN 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 I residue 107 CYS Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 16 LEU 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 141 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.097036 restraints weight = 23450.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.098797 restraints weight = 17203.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100129 restraints weight = 13815.672| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14154 Z= 0.183 Angle : 0.672 10.659 19413 Z= 0.342 Chirality : 0.044 0.220 2211 Planarity : 0.005 0.070 2464 Dihedral : 4.385 48.106 1871 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 5.81 % Allowed : 20.53 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.21), residues: 1700 helix: 1.49 (0.15), residues: 1196 sheet: None (None), residues: 0 loop : 0.15 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 62 HIS 0.006 0.002 HIS A 47 PHE 0.023 0.002 PHE E 18 TYR 0.022 0.002 TYR B 38 ARG 0.008 0.001 ARG F 127 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 925) hydrogen bonds : angle 4.33069 ( 2712) SS BOND : bond 0.00911 ( 4) SS BOND : angle 1.84516 ( 8) covalent geometry : bond 0.00436 (14150) covalent geometry : angle 0.67100 (19405) *********************** 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 504 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 416 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7535 (tpp-160) cc_final: 0.6582 (tpm170) REVERT: B 31 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 38 TYR cc_start: 0.8804 (m-10) cc_final: 0.8572 (m-10) REVERT: B 62 TRP cc_start: 0.8798 (t-100) cc_final: 0.8514 (t-100) REVERT: B 78 ASP cc_start: 0.8228 (t0) cc_final: 0.7953 (t70) REVERT: B 99 GLN cc_start: 0.9160 (tt0) cc_final: 0.8769 (tt0) REVERT: A 14 GLU cc_start: 0.8436 (pm20) cc_final: 0.8189 (pm20) REVERT: A 87 SER cc_start: 0.8687 (m) cc_final: 0.8461 (p) REVERT: A 95 LEU cc_start: 0.8427 (tt) cc_final: 0.8087 (tp) REVERT: C 55 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7894 (tt) REVERT: F 117 GLU cc_start: 0.5776 (tm-30) cc_final: 0.5489 (tm-30) REVERT: E 3 ILE cc_start: 0.9617 (mm) cc_final: 0.8495 (tt) REVERT: E 37 LEU cc_start: 0.9021 (tp) cc_final: 0.8611 (tp) REVERT: E 43 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8018 (mm-30) REVERT: E 99 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: H 82 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8006 (mtm-85) REVERT: G 39 ARG cc_start: 0.8439 (ttp-170) cc_final: 0.8111 (ttm170) REVERT: G 78 ASP cc_start: 0.8326 (t0) cc_final: 0.7671 (t0) REVERT: G 107 CYS cc_start: 0.9153 (m) cc_final: 0.8829 (m) REVERT: G 112 ARG cc_start: 0.8429 (ttm-80) cc_final: 0.8057 (ttm110) REVERT: G 121 SER cc_start: 0.8956 (t) cc_final: 0.8667 (t) REVERT: J 125 TRP cc_start: 0.9493 (t60) cc_final: 0.8758 (t60) REVERT: J 141 SER cc_start: 0.9629 (m) cc_final: 0.9120 (p) REVERT: I 57 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8035 (mp10) REVERT: I 117 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8194 (mm-30) REVERT: I 136 ASN cc_start: 0.8299 (p0) cc_final: 0.8034 (p0) REVERT: L 117 GLU cc_start: 0.7254 (tp30) cc_final: 0.7049 (tp30) REVERT: K 6 TYR cc_start: 0.8948 (m-80) cc_final: 0.8537 (m-80) REVERT: K 32 ASP cc_start: 0.7895 (t0) cc_final: 0.7659 (t0) REVERT: K 66 MET cc_start: 0.7925 (mmp) cc_final: 0.7663 (mmp) REVERT: K 86 VAL cc_start: 0.8742 (t) cc_final: 0.8473 (p) REVERT: K 88 TYR cc_start: 0.9175 (t80) cc_final: 0.8957 (t80) REVERT: K 108 LEU cc_start: 0.8898 (tt) cc_final: 0.8539 (tp) REVERT: K 117 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7118 (mp0) outliers start: 88 outliers final: 65 residues processed: 464 average time/residue: 0.2517 time to fit residues: 167.1254 Evaluate side-chains 470 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 400 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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 139 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 74 THR 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 D residue 121 SER Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 55 LEU 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 101 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 12 THR 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 99 GLN 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 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 59 ILE 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 89 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 THR 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 44 SER 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 89 VAL Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain L residue 87 SER 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 85 VAL Chi-restraints excluded: chain K residue 89 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 85 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.125392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.107574 restraints weight = 23082.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109647 restraints weight = 16259.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111065 restraints weight = 12676.400| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14154 Z= 0.173 Angle : 0.665 11.411 19413 Z= 0.339 Chirality : 0.044 0.218 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.345 50.955 1871 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 6.07 % Allowed : 20.92 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.21), residues: 1700 helix: 1.54 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.13 (0.31), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 62 HIS 0.005 0.002 HIS J 104 PHE 0.025 0.002 PHE C 18 TYR 0.021 0.002 TYR E 88 ARG 0.010 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 925) hydrogen bonds : angle 4.28072 ( 2712) SS BOND : bond 0.01046 ( 4) SS BOND : angle 1.61439 ( 8) covalent geometry : bond 0.00411 (14150) covalent geometry : angle 0.66459 (19405) *********************** 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 518 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 426 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.6664 (tpm170) REVERT: B 31 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8709 (mt) REVERT: B 38 TYR cc_start: 0.8805 (m-10) cc_final: 0.8509 (m-10) REVERT: B 78 ASP cc_start: 0.8279 (t0) cc_final: 0.8054 (t70) REVERT: B 96 LYS cc_start: 0.8606 (ttmt) cc_final: 0.8328 (ttmm) REVERT: B 99 GLN cc_start: 0.9160 (tt0) cc_final: 0.8730 (tt0) REVERT: A 14 GLU cc_start: 0.8409 (pm20) cc_final: 0.8177 (pm20) REVERT: A 23 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7105 (p90) REVERT: A 29 ASP cc_start: 0.5717 (t70) cc_final: 0.5456 (t0) REVERT: D 46 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7813 (mm-30) REVERT: C 55 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7853 (tt) REVERT: C 64 ASP cc_start: 0.8117 (m-30) cc_final: 0.7903 (m-30) REVERT: C 75 ASN cc_start: 0.7205 (m-40) cc_final: 0.6713 (t0) REVERT: F 117 GLU cc_start: 0.5750 (tm-30) cc_final: 0.5432 (tm-30) REVERT: E 3 ILE cc_start: 0.9667 (mm) cc_final: 0.8590 (tt) REVERT: E 28 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7843 (tpp-160) REVERT: E 37 LEU cc_start: 0.9035 (tp) cc_final: 0.8605 (tp) REVERT: E 43 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7972 (mm-30) REVERT: E 99 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: H 8 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6988 (tm-30) REVERT: H 70 THR cc_start: 0.8934 (m) cc_final: 0.8445 (p) REVERT: H 77 GLU cc_start: 0.7018 (mp0) cc_final: 0.6709 (mp0) REVERT: H 124 VAL cc_start: 0.9528 (t) cc_final: 0.9205 (p) REVERT: G 39 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.8145 (ttm170) REVERT: G 78 ASP cc_start: 0.8431 (t0) cc_final: 0.7619 (t0) REVERT: G 107 CYS cc_start: 0.9173 (m) cc_final: 0.8922 (m) REVERT: G 112 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8014 (ttm110) REVERT: G 121 SER cc_start: 0.8951 (t) cc_final: 0.8667 (t) REVERT: J 81 SER cc_start: 0.7721 (m) cc_final: 0.7455 (p) REVERT: J 125 TRP cc_start: 0.9509 (t60) cc_final: 0.8774 (t60) REVERT: J 141 SER cc_start: 0.9648 (m) cc_final: 0.9107 (p) REVERT: I 57 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: I 107 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8435 (t) REVERT: I 136 ASN cc_start: 0.8392 (p0) cc_final: 0.8148 (p0) REVERT: L 28 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7350 (tpp-160) REVERT: L 66 MET cc_start: 0.8402 (tpp) cc_final: 0.7919 (tpp) REVERT: L 117 GLU cc_start: 0.7268 (tp30) cc_final: 0.7040 (tp30) REVERT: K 6 TYR cc_start: 0.8971 (m-80) cc_final: 0.8423 (m-80) REVERT: K 66 MET cc_start: 0.7926 (mmp) cc_final: 0.7614 (mmp) REVERT: K 86 VAL cc_start: 0.8871 (t) cc_final: 0.8618 (p) REVERT: K 108 LEU cc_start: 0.8908 (tt) cc_final: 0.8587 (tp) REVERT: K 117 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: K 118 TYR cc_start: 0.9031 (t80) cc_final: 0.8281 (t80) outliers start: 92 outliers final: 65 residues processed: 475 average time/residue: 0.2487 time to fit residues: 170.7893 Evaluate side-chains 482 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 409 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 67 THR 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 121 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 VAL 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 67 THR Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 140 LEU 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 87 SER Chi-restraints excluded: chain H residue 121 SER 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 86 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 26 SER 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 44 SER Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL 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 I residue 120 VAL Chi-restraints excluded: chain L residue 16 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 85 VAL 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 135 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.091772 restraints weight = 24091.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.093594 restraints weight = 17323.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094919 restraints weight = 13838.595| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14154 Z= 0.221 Angle : 0.715 10.815 19413 Z= 0.364 Chirality : 0.046 0.215 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.473 53.862 1871 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 6.73 % Allowed : 21.12 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1700 helix: 1.43 (0.15), residues: 1186 sheet: None (None), residues: 0 loop : -0.09 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 62 HIS 0.007 0.002 HIS K 104 PHE 0.030 0.002 PHE K 110 TYR 0.018 0.002 TYR K 88 ARG 0.010 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 925) hydrogen bonds : angle 4.35690 ( 2712) SS BOND : bond 0.00937 ( 4) SS BOND : angle 1.75896 ( 8) covalent geometry : bond 0.00531 (14150) covalent geometry : angle 0.71395 (19405) *********************** 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 531 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 429 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.6738 (tpm170) REVERT: B 31 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8729 (mt) REVERT: B 38 TYR cc_start: 0.8867 (m-10) cc_final: 0.8622 (m-10) REVERT: B 96 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8326 (ttmm) REVERT: B 99 GLN cc_start: 0.9245 (tt0) cc_final: 0.8803 (tt0) REVERT: A 14 GLU cc_start: 0.8421 (pm20) cc_final: 0.8051 (pm20) REVERT: A 118 TYR cc_start: 0.9096 (t80) cc_final: 0.8814 (t80) REVERT: D 61 CYS cc_start: 0.7078 (m) cc_final: 0.6722 (m) REVERT: C 55 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7925 (tt) REVERT: C 64 ASP cc_start: 0.8149 (m-30) cc_final: 0.7865 (m-30) REVERT: C 75 ASN cc_start: 0.7320 (m-40) cc_final: 0.6797 (t0) REVERT: F 29 ASP cc_start: 0.8734 (m-30) cc_final: 0.8453 (m-30) REVERT: F 66 MET cc_start: 0.7407 (mmt) cc_final: 0.7130 (mmm) REVERT: E 3 ILE cc_start: 0.9717 (mm) cc_final: 0.8643 (tt) REVERT: E 28 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8163 (tpp-160) REVERT: E 43 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7943 (mm-30) REVERT: E 95 LEU cc_start: 0.8869 (tt) cc_final: 0.8639 (tp) REVERT: E 99 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8682 (mt0) REVERT: H 70 THR cc_start: 0.9008 (m) cc_final: 0.8528 (p) REVERT: H 77 GLU cc_start: 0.7135 (mp0) cc_final: 0.6715 (mp0) REVERT: G 39 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.8074 (ttm170) REVERT: G 82 ARG cc_start: 0.8225 (ptp90) cc_final: 0.7966 (ptp90) REVERT: G 96 LYS cc_start: 0.7920 (tttt) cc_final: 0.7645 (ttpt) REVERT: G 112 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8178 (ttm110) REVERT: G 121 SER cc_start: 0.8970 (t) cc_final: 0.8662 (t) REVERT: J 66 MET cc_start: 0.8374 (mmm) cc_final: 0.8061 (tpp) REVERT: J 67 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9130 (p) REVERT: J 81 SER cc_start: 0.7730 (m) cc_final: 0.7384 (p) REVERT: J 141 SER cc_start: 0.9588 (m) cc_final: 0.9203 (p) REVERT: I 57 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: I 75 ASN cc_start: 0.8000 (m110) cc_final: 0.7665 (m110) REVERT: I 136 ASN cc_start: 0.8773 (p0) cc_final: 0.8544 (p0) REVERT: L 28 ARG cc_start: 0.8336 (mmm160) cc_final: 0.7385 (tpp-160) REVERT: L 39 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7947 (tpp80) REVERT: L 117 GLU cc_start: 0.7433 (tp30) cc_final: 0.7069 (tp30) REVERT: K 6 TYR cc_start: 0.9065 (m-80) cc_final: 0.8829 (m-80) REVERT: K 66 MET cc_start: 0.8008 (mmp) cc_final: 0.7717 (mmp) REVERT: K 86 VAL cc_start: 0.8884 (t) cc_final: 0.8627 (p) REVERT: K 117 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: K 118 TYR cc_start: 0.9072 (t80) cc_final: 0.8311 (t80) outliers start: 102 outliers final: 77 residues processed: 481 average time/residue: 0.2470 time to fit residues: 170.8992 Evaluate side-chains 493 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 409 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 67 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ILE 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 57 GLN Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 86 VAL 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 124 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain F residue 4 ASP 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 101 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 VAL 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 67 THR Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 101 LEU 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 87 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 126 ILE 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 74 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 THR 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 72 VAL 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 I residue 120 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 87 SER 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 85 VAL 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 63 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094784 restraints weight = 23597.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.096583 restraints weight = 17295.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097843 restraints weight = 13837.226| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14154 Z= 0.149 Angle : 0.678 12.375 19413 Z= 0.340 Chirality : 0.043 0.225 2211 Planarity : 0.005 0.064 2464 Dihedral : 4.341 57.367 1871 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 4.49 % Allowed : 24.49 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1700 helix: 1.51 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.07 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 62 HIS 0.005 0.001 HIS L 51 PHE 0.027 0.001 PHE A 23 TYR 0.023 0.002 TYR A 38 ARG 0.010 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 925) hydrogen bonds : angle 4.21458 ( 2712) SS BOND : bond 0.00894 ( 4) SS BOND : angle 1.44109 ( 8) covalent geometry : bond 0.00345 (14150) covalent geometry : angle 0.67701 (19405) *********************** 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 501 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 433 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8632 (mt) REVERT: B 38 TYR cc_start: 0.8783 (m-10) cc_final: 0.8499 (m-10) REVERT: B 96 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8258 (ttmm) REVERT: B 99 GLN cc_start: 0.9190 (tt0) cc_final: 0.8728 (tt0) REVERT: A 14 GLU cc_start: 0.8487 (pm20) cc_final: 0.8132 (pm20) REVERT: D 26 SER cc_start: 0.8723 (t) cc_final: 0.8209 (p) REVERT: C 21 SER cc_start: 0.8813 (m) cc_final: 0.8048 (p) REVERT: C 55 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7823 (tt) REVERT: C 64 ASP cc_start: 0.8113 (m-30) cc_final: 0.7652 (m-30) REVERT: C 75 ASN cc_start: 0.7287 (m-40) cc_final: 0.6582 (m110) REVERT: C 90 ASN cc_start: 0.9133 (t0) cc_final: 0.8526 (t0) REVERT: E 3 ILE cc_start: 0.9742 (mm) cc_final: 0.8648 (tt) REVERT: E 28 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (tpp-160) REVERT: E 37 LEU cc_start: 0.8824 (tp) cc_final: 0.8541 (tp) REVERT: E 43 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7901 (mm-30) REVERT: E 99 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: E 112 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7673 (ttp-110) REVERT: H 70 THR cc_start: 0.8925 (m) cc_final: 0.8439 (p) REVERT: H 77 GLU cc_start: 0.7066 (mp0) cc_final: 0.6673 (mp0) REVERT: H 121 SER cc_start: 0.9485 (OUTLIER) cc_final: 0.9261 (t) REVERT: G 39 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8025 (ttm170) REVERT: G 78 ASP cc_start: 0.8427 (t0) cc_final: 0.7407 (t0) REVERT: G 121 SER cc_start: 0.8885 (t) cc_final: 0.8637 (t) REVERT: J 66 MET cc_start: 0.8495 (mmm) cc_final: 0.8290 (tpp) REVERT: J 81 SER cc_start: 0.7617 (m) cc_final: 0.7303 (p) REVERT: J 141 SER cc_start: 0.9655 (m) cc_final: 0.9227 (p) REVERT: I 7 LYS cc_start: 0.9007 (tppp) cc_final: 0.8393 (tptp) REVERT: I 57 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7937 (mp10) REVERT: I 75 ASN cc_start: 0.7977 (m110) cc_final: 0.7657 (m110) REVERT: I 107 CYS cc_start: 0.8807 (m) cc_final: 0.8386 (t) REVERT: L 28 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7355 (tpp-160) REVERT: L 66 MET cc_start: 0.8435 (tpp) cc_final: 0.8069 (tpp) REVERT: L 117 GLU cc_start: 0.7266 (tp30) cc_final: 0.6982 (tp30) REVERT: K 6 TYR cc_start: 0.8976 (m-80) cc_final: 0.8713 (m-80) REVERT: K 86 VAL cc_start: 0.8875 (t) cc_final: 0.8616 (p) REVERT: K 117 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: K 118 TYR cc_start: 0.9140 (t80) cc_final: 0.8307 (t80) outliers start: 68 outliers final: 54 residues processed: 468 average time/residue: 0.2483 time to fit residues: 166.0324 Evaluate side-chains 476 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 415 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 87 SER 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 59 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 8 GLU 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 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 THR 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 143 LEU 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 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 121 SER 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 74 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 89 VAL 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 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain L residue 16 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 85 VAL 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 135 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 143 optimal weight: 0.0570 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3370 r_free = 0.3370 target = 0.123124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105111 restraints weight = 22917.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.107214 restraints weight = 16109.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108634 restraints weight = 12526.114| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.5302 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= 0.161 Angle : 0.698 11.950 19413 Z= 0.349 Chirality : 0.044 0.231 2211 Planarity : 0.005 0.063 2464 Dihedral : 4.330 59.810 1871 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.71 % Rotamer: Outliers : 5.15 % Allowed : 24.55 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1700 helix: 1.53 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 62 HIS 0.004 0.001 HIS J 104 PHE 0.027 0.002 PHE A 23 TYR 0.021 0.002 TYR A 38 ARG 0.011 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 925) hydrogen bonds : angle 4.23471 ( 2712) SS BOND : bond 0.00860 ( 4) SS BOND : angle 1.43744 ( 8) covalent geometry : bond 0.00379 (14150) covalent geometry : angle 0.69785 (19405) *********************** 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 497 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 419 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 28 ARG cc_start: 0.7167 (tpp-160) cc_final: 0.6348 (tpm170) REVERT: B 31 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8501 (mt) REVERT: B 38 TYR cc_start: 0.8785 (m-10) cc_final: 0.8511 (m-10) REVERT: B 96 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8190 (ttpp) REVERT: B 99 GLN cc_start: 0.9193 (tt0) cc_final: 0.8745 (tt0) REVERT: A 14 GLU cc_start: 0.8434 (pm20) cc_final: 0.8082 (pm20) REVERT: A 77 GLU cc_start: 0.7138 (mp0) cc_final: 0.6746 (mp0) REVERT: C 21 SER cc_start: 0.8808 (m) cc_final: 0.8115 (p) REVERT: C 55 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7829 (tt) REVERT: C 75 ASN cc_start: 0.7293 (m-40) cc_final: 0.6628 (m110) REVERT: C 90 ASN cc_start: 0.9128 (t0) cc_final: 0.8559 (t0) REVERT: E 3 ILE cc_start: 0.9753 (mm) cc_final: 0.8681 (tt) REVERT: E 28 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8121 (tpp-160) REVERT: E 43 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 99 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8518 (mt0) REVERT: E 112 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7695 (ttp-110) REVERT: H 70 THR cc_start: 0.8912 (m) cc_final: 0.8421 (p) REVERT: H 77 GLU cc_start: 0.7044 (mp0) cc_final: 0.6670 (mp0) REVERT: H 121 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9275 (t) REVERT: G 30 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8894 (mt) REVERT: G 39 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.7990 (ttm170) REVERT: G 121 SER cc_start: 0.8900 (t) cc_final: 0.8651 (t) REVERT: J 66 MET cc_start: 0.8392 (mmm) cc_final: 0.8126 (tpp) REVERT: J 81 SER cc_start: 0.7727 (m) cc_final: 0.7385 (p) REVERT: J 141 SER cc_start: 0.9606 (m) cc_final: 0.9274 (p) REVERT: I 57 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: I 75 ASN cc_start: 0.7999 (m110) cc_final: 0.7628 (m110) REVERT: L 28 ARG cc_start: 0.8300 (mmm160) cc_final: 0.7374 (tpp-160) REVERT: L 39 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7840 (tpp80) REVERT: L 66 MET cc_start: 0.8352 (tpp) cc_final: 0.7979 (mpp) REVERT: L 117 GLU cc_start: 0.7318 (tp30) cc_final: 0.6954 (tp30) REVERT: K 6 TYR cc_start: 0.9012 (m-80) cc_final: 0.8770 (m-80) REVERT: K 86 VAL cc_start: 0.8894 (t) cc_final: 0.8629 (p) REVERT: K 117 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: K 118 TYR cc_start: 0.9132 (t80) cc_final: 0.8288 (t80) outliers start: 78 outliers final: 64 residues processed: 462 average time/residue: 0.2474 time to fit residues: 163.8769 Evaluate side-chains 484 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 411 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 87 SER 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 59 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 8 GLU 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 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 THR 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 142 THR 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 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 30 LEU 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 74 THR 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 67 THR Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 89 VAL 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 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 107 CYS 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 85 VAL 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 110 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.0570 chunk 120 optimal weight: 9.9990 chunk 114 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 overall best weight: 3.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 90 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.093570 restraints weight = 23700.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.095282 restraints weight = 17643.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096349 restraints weight = 14352.109| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.5395 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= 0.166 Angle : 0.706 11.720 19413 Z= 0.353 Chirality : 0.044 0.230 2211 Planarity : 0.005 0.061 2464 Dihedral : 4.285 56.030 1870 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer: Outliers : 5.21 % Allowed : 24.42 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1700 helix: 1.50 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : -0.02 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 62 HIS 0.005 0.001 HIS J 104 PHE 0.026 0.002 PHE A 23 TYR 0.021 0.002 TYR F 88 ARG 0.010 0.001 ARG F 28 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 925) hydrogen bonds : angle 4.22393 ( 2712) SS BOND : bond 0.00880 ( 4) SS BOND : angle 1.45230 ( 8) covalent geometry : bond 0.00392 (14150) covalent geometry : angle 0.70547 (19405) ********************** 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 501 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 422 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.6566 (t80) REVERT: B 28 ARG cc_start: 0.7190 (tpp-160) cc_final: 0.6366 (tpm170) REVERT: B 31 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 38 TYR cc_start: 0.8792 (m-10) cc_final: 0.8527 (m-10) REVERT: B 96 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8185 (ttpp) REVERT: B 99 GLN cc_start: 0.9195 (tt0) cc_final: 0.8750 (tt0) REVERT: A 14 GLU cc_start: 0.8410 (pm20) cc_final: 0.8062 (pm20) REVERT: A 77 GLU cc_start: 0.7103 (mp0) cc_final: 0.6752 (mp0) REVERT: C 21 SER cc_start: 0.8827 (m) cc_final: 0.8111 (p) REVERT: C 55 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7863 (tt) REVERT: C 60 LEU cc_start: 0.9268 (mm) cc_final: 0.9053 (mt) REVERT: C 75 ASN cc_start: 0.7309 (m-40) cc_final: 0.6650 (m110) REVERT: C 90 ASN cc_start: 0.9128 (t0) cc_final: 0.8574 (t0) REVERT: E 3 ILE cc_start: 0.9756 (mm) cc_final: 0.8720 (tt) REVERT: E 28 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8157 (tpp-160) REVERT: E 43 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7909 (mm-30) REVERT: E 99 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: H 8 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7049 (tm-30) REVERT: H 70 THR cc_start: 0.8911 (m) cc_final: 0.8436 (p) REVERT: H 77 GLU cc_start: 0.7031 (mp0) cc_final: 0.6639 (mp0) REVERT: G 30 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8794 (mt) REVERT: G 39 ARG cc_start: 0.8411 (ttp-170) cc_final: 0.7856 (ttm170) REVERT: G 121 SER cc_start: 0.8990 (t) cc_final: 0.8673 (t) REVERT: J 66 MET cc_start: 0.8365 (mmm) cc_final: 0.8126 (tpp) REVERT: J 81 SER cc_start: 0.7711 (m) cc_final: 0.7371 (p) REVERT: J 141 SER cc_start: 0.9638 (m) cc_final: 0.9268 (p) REVERT: I 57 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: I 75 ASN cc_start: 0.8026 (m110) cc_final: 0.7649 (m110) REVERT: L 28 ARG cc_start: 0.8280 (mmm160) cc_final: 0.7378 (tpp-160) REVERT: L 39 ARG cc_start: 0.8144 (tpp80) cc_final: 0.7859 (tpp80) REVERT: L 66 MET cc_start: 0.8352 (tpp) cc_final: 0.7994 (mpp) REVERT: L 117 GLU cc_start: 0.7288 (tp30) cc_final: 0.6954 (tp30) REVERT: K 6 TYR cc_start: 0.9027 (m-80) cc_final: 0.8784 (m-80) REVERT: K 86 VAL cc_start: 0.8896 (t) cc_final: 0.8652 (p) REVERT: K 117 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: K 118 TYR cc_start: 0.9170 (t80) cc_final: 0.8287 (t80) outliers start: 79 outliers final: 64 residues processed: 464 average time/residue: 0.2429 time to fit residues: 161.5537 Evaluate side-chains 486 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 414 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE 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 70 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 8 GLU 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 67 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain D residue 8 GLU 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 22 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 THR 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 142 THR 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 99 GLN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain G residue 30 LEU 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 74 THR 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 67 THR Chi-restraints excluded: chain J residue 89 VAL 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 72 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 107 CYS 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 85 VAL 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 8 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 140 optimal weight: 0.2980 chunk 16 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108226 restraints weight = 22719.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.110315 restraints weight = 16003.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111737 restraints weight = 12500.752| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5407 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= 0.139 Angle : 0.684 11.836 19413 Z= 0.340 Chirality : 0.043 0.236 2211 Planarity : 0.005 0.061 2464 Dihedral : 4.088 44.506 1870 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.06 % Favored : 96.88 % Rotamer: Outliers : 4.22 % Allowed : 25.81 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1700 helix: 1.58 (0.15), residues: 1193 sheet: None (None), residues: 0 loop : 0.06 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 62 HIS 0.004 0.001 HIS L 51 PHE 0.024 0.001 PHE A 23 TYR 0.021 0.002 TYR F 88 ARG 0.011 0.001 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 925) hydrogen bonds : angle 4.16917 ( 2712) SS BOND : bond 0.00846 ( 4) SS BOND : angle 1.31148 ( 8) covalent geometry : bond 0.00317 (14150) covalent geometry : angle 0.68353 (19405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4468.37 seconds wall clock time: 78 minutes 55.94 seconds (4735.94 seconds total)