Starting phenix.real_space_refine on Thu Jul 31 09:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghs_40049/07_2025/8ghs_40049.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghs_40049/07_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_40049/07_2025/8ghs_40049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghs_40049/07_2025/8ghs_40049.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghs_40049/07_2025/8ghs_40049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghs_40049/07_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-5711/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: 8.01, per 1000 atoms: 0.58 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: 3.85 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: 1.26 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: 3.79 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.680 Find NCS groups from input model: 0.560 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.420 ------------------------------------------------------------------------------- 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 : 1.636 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: 0.2584 time to fit residues: 194.5040 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 : 1.590 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.129738 restraints weight = 22139.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132030 restraints weight = 15093.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133623 restraints weight = 11466.888| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- 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 9.602 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 4.56766 ( 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 : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ASP cc_start: 0.7862 (t0) cc_final: 0.6242 (m-30) REVERT: B 99 GLN cc_start: 0.9016 (tt0) cc_final: 0.8376 (tt0) REVERT: A 87 SER cc_start: 0.8862 (m) cc_final: 0.8513 (p) REVERT: A 88 TYR cc_start: 0.7938 (t80) cc_final: 0.7513 (t80) REVERT: D 8 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8027 (tm-30) REVERT: D 61 CYS cc_start: 0.6635 (m) cc_final: 0.6179 (m) REVERT: C 7 LYS cc_start: 0.9167 (tttm) cc_final: 0.8504 (ttmm) REVERT: C 9 PHE cc_start: 0.7917 (m-80) cc_final: 0.7633 (m-10) REVERT: F 7 LYS cc_start: 0.9170 (tttp) cc_final: 0.8926 (tttp) REVERT: F 19 LEU cc_start: 0.9288 (mt) cc_final: 0.9056 (mt) REVERT: F 96 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7921 (tmmt) REVERT: E 112 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7369 (ttm110) REVERT: E 117 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8166 (mm-30) REVERT: H 8 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6620 (tm-30) REVERT: H 22 ASP cc_start: 0.6669 (t70) cc_final: 0.6411 (t70) REVERT: H 82 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7519 (mmm-85) REVERT: H 125 TRP cc_start: 0.9015 (t60) cc_final: 0.8796 (t60) REVERT: G 14 GLU cc_start: 0.7525 (pt0) cc_final: 0.7306 (pt0) REVERT: G 17 SER cc_start: 0.9381 (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: 0.7443 (t0) cc_final: 0.6447 (t0) REVERT: J 8 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7826 (tm-30) REVERT: J 136 ASN cc_start: 0.8906 (p0) cc_final: 0.8696 (p0) REVERT: I 7 LYS cc_start: 0.8988 (tppp) cc_final: 0.8689 (tptp) REVERT: I 64 ASP cc_start: 0.8637 (m-30) cc_final: 0.8169 (m-30) REVERT: L 66 MET cc_start: 0.8253 (mmm) cc_final: 0.7962 (tpp) REVERT: K 59 ILE cc_start: 0.8321 (mm) cc_final: 0.8100 (mm) REVERT: K 66 MET cc_start: 0.7239 (mmp) cc_final: 0.6789 (mmt) REVERT: K 88 TYR cc_start: 0.8918 (t80) cc_final: 0.8538 (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: 0.6949 (mp0) outliers start: 40 outliers final: 25 residues processed: 444 average time/residue: 0.2673 time to fit residues: 170.7440 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 : 1.607 ------------------------------------------------------------------------------- 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: 0.7980 chunk 100 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 15 optimal weight: 0.0970 chunk 134 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- 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 104 HIS G 136 ASN J 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117554 restraints weight = 22487.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.119780 restraints weight = 15522.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121269 restraints weight = 11940.376| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3431 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= 0.176 Angle : 0.669 10.401 19413 Z= 0.340 Chirality : 0.045 0.238 2211 Planarity : 0.005 0.067 2464 Dihedral : 4.318 42.419 1871 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 4.29 % Allowed : 15.31 % Favored : 80.40 % 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: 1.69 (0.21), residues: 1700 helix: 1.59 (0.15), residues: 1189 sheet: None (None), residues: 0 loop : 0.16 (0.31), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 102 HIS 0.009 0.002 HIS A 47 PHE 0.022 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 0.04390 ( 925) hydrogen bonds : angle 4.42812 ( 2712) SS BOND : bond 0.01017 ( 4) SS BOND : angle 1.80203 ( 8) covalent geometry : bond 0.00410 (14150) covalent geometry : angle 0.66767 (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 473 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 408 time to evaluate : 1.498 Fit side-chains revert: symmetry clash REVERT: B 78 ASP cc_start: 0.8006 (t0) cc_final: 0.7758 (t0) REVERT: B 99 GLN cc_start: 0.9150 (tt0) cc_final: 0.8637 (tt0) REVERT: A 14 GLU cc_start: 0.8103 (pm20) cc_final: 0.7840 (pm20) REVERT: A 87 SER cc_start: 0.8830 (m) cc_final: 0.8494 (p) REVERT: A 88 TYR cc_start: 0.8227 (t80) cc_final: 0.7915 (t80) REVERT: D 8 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 61 CYS cc_start: 0.6799 (m) cc_final: 0.6367 (m) REVERT: D 96 LYS cc_start: 0.8795 (tttm) cc_final: 0.8415 (tttm) REVERT: D 99 GLN cc_start: 0.8088 (tt0) cc_final: 0.7870 (pt0) REVERT: C 7 LYS cc_start: 0.9218 (tttm) cc_final: 0.8772 (tttp) REVERT: C 48 CYS cc_start: 0.8417 (p) cc_final: 0.8197 (m) REVERT: F 59 ILE cc_start: 0.8123 (pt) cc_final: 0.7810 (mt) REVERT: F 126 ILE cc_start: 0.9460 (tp) cc_final: 0.9181 (tp) REVERT: E 99 GLN cc_start: 0.8852 (mt0) cc_final: 0.8537 (mt0) REVERT: E 117 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8221 (mm-30) REVERT: E 118 TYR cc_start: 0.9062 (t80) cc_final: 0.8719 (t80) REVERT: H 55 LEU cc_start: 0.8405 (tt) cc_final: 0.8190 (tt) REVERT: H 60 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8665 (mm) REVERT: H 82 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7493 (mmm-85) REVERT: G 14 GLU cc_start: 0.7913 (pt0) cc_final: 0.7437 (pt0) REVERT: G 17 SER cc_start: 0.9408 (p) cc_final: 0.9088 (t) REVERT: G 78 ASP cc_start: 0.7675 (t0) cc_final: 0.6479 (t0) REVERT: G 121 SER cc_start: 0.8794 (t) cc_final: 0.8276 (p) REVERT: J 8 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8147 (tm-30) REVERT: J 141 SER cc_start: 0.9564 (m) cc_final: 0.8960 (p) REVERT: I 7 LYS cc_start: 0.8932 (tppp) cc_final: 0.8350 (tptp) REVERT: I 14 GLU cc_start: 0.7099 (pp20) cc_final: 0.6843 (pp20) REVERT: I 117 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8091 (mm-30) REVERT: L 66 MET cc_start: 0.8419 (mmm) cc_final: 0.7803 (tpp) REVERT: L 117 GLU cc_start: 0.7156 (tp30) cc_final: 0.6920 (tp30) REVERT: K 117 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7936 (mp0) outliers start: 65 outliers final: 48 residues processed: 435 average time/residue: 0.2775 time to fit residues: 174.1399 Evaluate side-chains 428 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 378 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 12 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 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 124 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 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 G residue 86 VAL Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain L residue 16 LEU Chi-restraints excluded: chain L residue 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 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: 0.0670 chunk 130 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- 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 J 92 ASN I 99 GLN L 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098319 restraints weight = 23389.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100178 restraints weight = 17071.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.101441 restraints weight = 13678.757| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14154 Z= 0.208 Angle : 0.692 11.761 19413 Z= 0.356 Chirality : 0.046 0.225 2211 Planarity : 0.005 0.045 2464 Dihedral : 4.447 44.320 1871 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 5.48 % Allowed : 18.68 % Favored : 75.84 % 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 : 0.02 (0.31), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 71 HIS 0.007 0.002 HIS B 51 PHE 0.022 0.002 PHE C 18 TYR 0.022 0.002 TYR L 38 ARG 0.005 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04803 ( 925) hydrogen bonds : angle 4.41292 ( 2712) SS BOND : bond 0.01195 ( 4) SS BOND : angle 1.63680 ( 8) covalent geometry : bond 0.00499 (14150) covalent geometry : angle 0.69145 (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 505 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 422 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8740 (mt) REVERT: B 78 ASP cc_start: 0.8155 (t0) cc_final: 0.7701 (t0) REVERT: B 99 GLN cc_start: 0.9162 (tt0) cc_final: 0.8642 (tt0) REVERT: A 14 GLU cc_start: 0.8253 (pm20) cc_final: 0.7987 (pm20) REVERT: A 87 SER cc_start: 0.8790 (m) cc_final: 0.8512 (p) REVERT: D 60 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9136 (mm) REVERT: C 7 LYS cc_start: 0.9191 (tttm) cc_final: 0.8800 (tttp) REVERT: F 59 ILE cc_start: 0.8394 (pt) cc_final: 0.8178 (mt) REVERT: F 117 GLU cc_start: 0.4636 (tm-30) cc_final: 0.4181 (tm-30) REVERT: E 3 ILE cc_start: 0.9491 (mm) cc_final: 0.8337 (tt) REVERT: E 43 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8033 (mm-30) REVERT: E 99 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: H 8 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7081 (tm-30) REVERT: H 70 THR cc_start: 0.9025 (m) cc_final: 0.8496 (p) REVERT: H 82 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.7880 (mtm-85) REVERT: H 88 TYR cc_start: 0.8333 (t80) cc_final: 0.8117 (t80) REVERT: H 99 GLN cc_start: 0.8586 (tt0) cc_final: 0.8363 (tt0) REVERT: G 14 GLU cc_start: 0.7950 (pt0) cc_final: 0.7732 (pt0) REVERT: G 39 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.7877 (ttp-170) REVERT: G 40 ASP cc_start: 0.8331 (m-30) cc_final: 0.8058 (m-30) REVERT: G 78 ASP cc_start: 0.8031 (t0) cc_final: 0.7279 (t0) REVERT: G 107 CYS cc_start: 0.9073 (m) cc_final: 0.8674 (m) REVERT: G 121 SER cc_start: 0.8834 (t) cc_final: 0.8285 (p) REVERT: J 8 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8382 (tm-30) REVERT: J 125 TRP cc_start: 0.9462 (t60) cc_final: 0.8740 (t60) REVERT: J 136 ASN cc_start: 0.9025 (p0) cc_final: 0.8809 (p0) REVERT: J 141 SER cc_start: 0.9611 (m) cc_final: 0.9029 (p) REVERT: I 57 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: I 136 ASN cc_start: 0.8243 (p0) cc_final: 0.7978 (p0) REVERT: L 39 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7860 (tpp80) REVERT: L 145 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6886 (mm-30) REVERT: K 6 TYR cc_start: 0.8915 (m-80) cc_final: 0.8670 (m-80) REVERT: K 70 THR cc_start: 0.8435 (m) cc_final: 0.8208 (p) REVERT: K 86 VAL cc_start: 0.8693 (t) cc_final: 0.8489 (p) REVERT: K 88 TYR cc_start: 0.9211 (t80) cc_final: 0.8904 (t80) REVERT: K 117 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.6941 (mp0) outliers start: 83 outliers final: 62 residues processed: 463 average time/residue: 0.3116 time to fit residues: 209.0389 Evaluate side-chains 464 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 397 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 46 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 74 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 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 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 47 HIS Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 65 LEU 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 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 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 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 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 105 ILE Chi-restraints excluded: chain K residue 117 GLU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 141 SER Rotamers are restrained with sigma=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: 3.9990 chunk 70 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.114633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.096711 restraints weight = 23457.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.098504 restraints weight = 17226.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.099755 restraints weight = 13875.911| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4520 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= 0.188 Angle : 0.677 11.049 19413 Z= 0.344 Chirality : 0.044 0.217 2211 Planarity : 0.005 0.070 2464 Dihedral : 4.397 47.517 1871 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 5.87 % Allowed : 20.66 % Favored : 73.47 % 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: 1.54 (0.21), residues: 1700 helix: 1.49 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : 0.06 (0.31), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 62 HIS 0.006 0.002 HIS A 47 PHE 0.023 0.002 PHE C 18 TYR 0.023 0.002 TYR B 38 ARG 0.006 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 925) hydrogen bonds : angle 4.34268 ( 2712) SS BOND : bond 0.01075 ( 4) SS BOND : angle 1.91851 ( 8) covalent geometry : bond 0.00449 (14150) covalent geometry : angle 0.67562 (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 507 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 418 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.6582 (tpm170) REVERT: B 31 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8727 (mt) REVERT: B 38 TYR cc_start: 0.8820 (m-10) cc_final: 0.8553 (m-10) REVERT: B 66 MET cc_start: 0.8361 (mmt) cc_final: 0.7781 (mmm) REVERT: B 78 ASP cc_start: 0.8216 (t0) cc_final: 0.7965 (t70) REVERT: B 99 GLN cc_start: 0.9161 (tt0) cc_final: 0.8761 (tt0) REVERT: A 14 GLU cc_start: 0.8427 (pm20) cc_final: 0.8207 (pm20) REVERT: A 87 SER cc_start: 0.8706 (m) cc_final: 0.8471 (p) REVERT: A 95 LEU cc_start: 0.8441 (tt) cc_final: 0.8102 (tp) REVERT: D 60 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9166 (mm) REVERT: C 55 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7917 (tt) REVERT: F 117 GLU cc_start: 0.5790 (tm-30) cc_final: 0.5515 (tm-30) REVERT: E 3 ILE cc_start: 0.9575 (mm) cc_final: 0.8455 (tt) REVERT: E 43 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8014 (mm-30) REVERT: E 99 GLN cc_start: 0.8944 (mt0) cc_final: 0.8667 (mt0) REVERT: H 82 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: G 14 GLU cc_start: 0.8010 (pt0) cc_final: 0.7780 (pt0) REVERT: G 39 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.8000 (ttm170) REVERT: G 78 ASP cc_start: 0.8312 (t0) cc_final: 0.7662 (t0) REVERT: G 107 CYS cc_start: 0.9147 (m) cc_final: 0.8815 (m) REVERT: G 112 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8048 (ttm110) REVERT: G 121 SER cc_start: 0.8966 (t) cc_final: 0.8678 (t) REVERT: J 125 TRP cc_start: 0.9497 (t60) cc_final: 0.8761 (t60) REVERT: J 141 SER cc_start: 0.9632 (m) cc_final: 0.9125 (p) REVERT: I 57 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: I 136 ASN cc_start: 0.8327 (p0) cc_final: 0.8075 (p0) REVERT: L 117 GLU cc_start: 0.7391 (tp30) cc_final: 0.7175 (tp30) REVERT: K 6 TYR cc_start: 0.8960 (m-80) cc_final: 0.8546 (m-80) REVERT: K 32 ASP cc_start: 0.7932 (t0) cc_final: 0.7717 (t0) REVERT: K 66 MET cc_start: 0.7525 (mmp) cc_final: 0.7232 (mmp) REVERT: K 86 VAL cc_start: 0.8727 (t) cc_final: 0.8455 (p) REVERT: K 88 TYR cc_start: 0.9187 (t80) cc_final: 0.8983 (t80) REVERT: K 117 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7125 (mp0) outliers start: 89 outliers final: 65 residues processed: 465 average time/residue: 0.3301 time to fit residues: 223.6704 Evaluate side-chains 469 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 399 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 70 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 95 LEU Chi-restraints excluded: chain D residue 124 VAL 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 60 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 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 87 SER 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 G residue 72 VAL Chi-restraints excluded: chain G residue 74 THR 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 30 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 67 THR 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 105 ILE 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: 0.9990 chunk 151 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 K 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106175 restraints weight = 23149.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108269 restraints weight = 16172.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.109734 restraints weight = 12590.978| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14154 Z= 0.172 Angle : 0.669 11.278 19413 Z= 0.340 Chirality : 0.044 0.216 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.348 50.594 1871 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 6.01 % Allowed : 21.19 % Favored : 72.81 % 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: 1.60 (0.21), residues: 1700 helix: 1.52 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.09 (0.31), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 62 HIS 0.005 0.001 HIS A 47 PHE 0.024 0.002 PHE C 18 TYR 0.018 0.002 TYR A 38 ARG 0.006 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 925) hydrogen bonds : angle 4.27226 ( 2712) SS BOND : bond 0.00820 ( 4) SS BOND : angle 1.65604 ( 8) covalent geometry : bond 0.00408 (14150) covalent geometry : angle 0.66877 (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 519 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 428 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7601 (tpp-160) cc_final: 0.6650 (tpm170) REVERT: B 31 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8656 (mt) REVERT: B 38 TYR cc_start: 0.8799 (m-10) cc_final: 0.8525 (m-10) REVERT: B 66 MET cc_start: 0.8336 (mmt) cc_final: 0.7933 (mmm) REVERT: B 96 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8309 (ttmm) REVERT: B 99 GLN cc_start: 0.9148 (tt0) cc_final: 0.8705 (tt0) REVERT: A 14 GLU cc_start: 0.8411 (pm20) cc_final: 0.8039 (pm20) REVERT: A 23 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7101 (p90) REVERT: A 29 ASP cc_start: 0.5720 (t70) cc_final: 0.5486 (t0) REVERT: A 62 TRP cc_start: 0.8063 (t-100) cc_final: 0.7491 (t-100) REVERT: D 96 LYS cc_start: 0.8781 (tttt) cc_final: 0.8456 (ttpt) REVERT: C 55 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7871 (tt) REVERT: C 75 ASN cc_start: 0.7222 (m-40) cc_final: 0.6714 (t0) REVERT: F 29 ASP cc_start: 0.8647 (m-30) cc_final: 0.8446 (m-30) REVERT: F 117 GLU cc_start: 0.5735 (tm-30) cc_final: 0.5446 (tm-30) REVERT: E 3 ILE cc_start: 0.9663 (mm) cc_final: 0.8604 (tt) REVERT: E 28 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7858 (tpp-160) REVERT: E 37 LEU cc_start: 0.8973 (tp) cc_final: 0.8691 (tp) REVERT: E 43 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7967 (mm-30) REVERT: E 99 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: H 70 THR cc_start: 0.8955 (m) cc_final: 0.8456 (p) REVERT: H 77 GLU cc_start: 0.7030 (mp0) cc_final: 0.6711 (mp0) REVERT: G 39 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.7947 (ttm170) REVERT: G 78 ASP cc_start: 0.8419 (t0) cc_final: 0.7604 (t0) REVERT: G 107 CYS cc_start: 0.9155 (m) cc_final: 0.8891 (m) REVERT: G 112 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8011 (ttm110) REVERT: G 121 SER cc_start: 0.8957 (t) cc_final: 0.8679 (t) REVERT: J 125 TRP cc_start: 0.9512 (t60) cc_final: 0.8779 (t60) REVERT: J 141 SER cc_start: 0.9649 (m) cc_final: 0.9109 (p) REVERT: I 57 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7987 (mp10) REVERT: I 107 CYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8436 (t) REVERT: I 136 ASN cc_start: 0.8412 (p0) cc_final: 0.8191 (p0) REVERT: L 117 GLU cc_start: 0.7236 (tp30) cc_final: 0.7004 (tp30) REVERT: K 6 TYR cc_start: 0.8973 (m-80) cc_final: 0.8413 (m-80) REVERT: K 66 MET cc_start: 0.7937 (mmp) cc_final: 0.7627 (mmp) REVERT: K 86 VAL cc_start: 0.8863 (t) cc_final: 0.8618 (p) REVERT: K 88 TYR cc_start: 0.9196 (t80) cc_final: 0.8944 (t80) REVERT: K 117 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: K 118 TYR cc_start: 0.9035 (t80) cc_final: 0.8292 (t80) outliers start: 91 outliers final: 64 residues processed: 479 average time/residue: 0.2636 time to fit residues: 181.7105 Evaluate side-chains 483 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 411 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 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 23 PHE 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 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 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 47 HIS 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 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 15 LEU 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 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 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 Chi-restraints excluded: chain K residue 141 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 135 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.0010 chunk 107 optimal weight: 7.9990 overall best weight: 2.7190 ------------------------------------------------------------------------------- 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 K 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107924 restraints weight = 22981.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.109972 restraints weight = 16154.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.111397 restraints weight = 12580.859| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14154 Z= 0.154 Angle : 0.665 10.525 19413 Z= 0.334 Chirality : 0.043 0.220 2211 Planarity : 0.005 0.071 2464 Dihedral : 4.289 53.156 1871 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.65 % Rotamer: Outliers : 5.61 % Allowed : 22.31 % Favored : 72.08 % 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: 1.56 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.12 (0.31), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 62 HIS 0.004 0.001 HIS A 47 PHE 0.033 0.001 PHE K 110 TYR 0.018 0.002 TYR F 88 ARG 0.011 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 925) hydrogen bonds : angle 4.22882 ( 2712) SS BOND : bond 0.00942 ( 4) SS BOND : angle 1.56004 ( 8) covalent geometry : bond 0.00362 (14150) covalent geometry : angle 0.66481 (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 524 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 439 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.7592 (tpp-160) cc_final: 0.7343 (tpp-160) REVERT: B 31 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8698 (mt) REVERT: B 38 TYR cc_start: 0.8782 (m-10) cc_final: 0.8528 (m-10) REVERT: B 96 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8242 (ttmm) REVERT: B 99 GLN cc_start: 0.9152 (tt0) cc_final: 0.8709 (tt0) REVERT: A 14 GLU cc_start: 0.8426 (pm20) cc_final: 0.8057 (pm20) REVERT: A 23 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7232 (p90) REVERT: A 62 TRP cc_start: 0.8050 (t-100) cc_final: 0.7502 (t-100) REVERT: D 46 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7826 (mm-30) REVERT: D 96 LYS cc_start: 0.8791 (tttt) cc_final: 0.8389 (tttt) REVERT: D 99 GLN cc_start: 0.7871 (tt0) cc_final: 0.7552 (pt0) REVERT: C 21 SER cc_start: 0.8776 (m) cc_final: 0.8105 (p) REVERT: C 55 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7822 (tt) REVERT: C 60 LEU cc_start: 0.9222 (mm) cc_final: 0.9009 (mt) REVERT: C 75 ASN cc_start: 0.7215 (m-40) cc_final: 0.6535 (m110) REVERT: C 90 ASN cc_start: 0.9095 (t0) cc_final: 0.8460 (t0) REVERT: F 29 ASP cc_start: 0.8657 (m-30) cc_final: 0.8430 (m-30) REVERT: F 117 GLU cc_start: 0.5551 (tm-30) cc_final: 0.5271 (tm-30) REVERT: E 3 ILE cc_start: 0.9729 (mm) cc_final: 0.8627 (tt) REVERT: E 28 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (tpp-160) REVERT: E 43 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7953 (mm-30) REVERT: E 99 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: H 60 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8650 (mm) REVERT: H 70 THR cc_start: 0.8909 (m) cc_final: 0.8416 (p) REVERT: H 77 GLU cc_start: 0.7070 (mp0) cc_final: 0.6666 (mp0) REVERT: G 30 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8903 (mt) REVERT: G 39 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.8067 (ttm170) REVERT: G 78 ASP cc_start: 0.8431 (t0) cc_final: 0.7568 (t0) REVERT: G 82 ARG cc_start: 0.8158 (ptp90) cc_final: 0.7671 (ptp90) REVERT: G 107 CYS cc_start: 0.9173 (m) cc_final: 0.8818 (m) REVERT: G 112 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8025 (ttm110) REVERT: G 121 SER cc_start: 0.8898 (t) cc_final: 0.8655 (t) REVERT: J 125 TRP cc_start: 0.9407 (t60) cc_final: 0.8632 (t60) REVERT: J 141 SER cc_start: 0.9582 (m) cc_final: 0.9144 (p) REVERT: I 57 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: I 107 CYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8399 (t) REVERT: I 136 ASN cc_start: 0.8416 (p0) cc_final: 0.8211 (p0) REVERT: L 28 ARG cc_start: 0.8315 (mmm160) cc_final: 0.7286 (tpp-160) REVERT: L 88 TYR cc_start: 0.8826 (t80) cc_final: 0.8542 (t80) REVERT: L 117 GLU cc_start: 0.7207 (tp30) cc_final: 0.6947 (tp30) REVERT: K 6 TYR cc_start: 0.8952 (m-80) cc_final: 0.8358 (m-80) REVERT: K 66 MET cc_start: 0.7906 (mmp) cc_final: 0.7624 (mmp) REVERT: K 86 VAL cc_start: 0.8884 (t) cc_final: 0.8615 (p) REVERT: K 99 GLN cc_start: 0.8202 (mt0) cc_final: 0.7856 (mt0) REVERT: K 117 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: K 118 TYR cc_start: 0.9095 (t80) cc_final: 0.8229 (t80) outliers start: 85 outliers final: 60 residues processed: 481 average time/residue: 0.2506 time to fit residues: 173.9278 Evaluate side-chains 485 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 415 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 70 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 140 LEU 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 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 47 HIS Chi-restraints excluded: chain F residue 55 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 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 12 THR 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 30 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 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 78 ASP Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.112540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094927 restraints weight = 23669.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.096670 restraints weight = 17455.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097874 restraints weight = 14034.485| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14154 Z= 0.157 Angle : 0.676 12.544 19413 Z= 0.338 Chirality : 0.043 0.226 2211 Planarity : 0.005 0.072 2464 Dihedral : 4.269 56.227 1871 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 5.48 % Allowed : 23.23 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : 0.11 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 62 HIS 0.004 0.001 HIS J 104 PHE 0.036 0.002 PHE K 110 TYR 0.023 0.002 TYR A 38 ARG 0.010 0.001 ARG L 39 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 925) hydrogen bonds : angle 4.20712 ( 2712) SS BOND : bond 0.00892 ( 4) SS BOND : angle 1.44749 ( 8) covalent geometry : bond 0.00370 (14150) covalent geometry : angle 0.67507 (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 514 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 431 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 38 TYR cc_start: 0.8776 (m-10) cc_final: 0.8514 (m-10) REVERT: B 66 MET cc_start: 0.8461 (mmm) cc_final: 0.8217 (mmm) REVERT: B 83 ASP cc_start: 0.8396 (p0) cc_final: 0.8105 (p0) REVERT: B 96 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8230 (ttmm) REVERT: B 99 GLN cc_start: 0.9169 (tt0) cc_final: 0.8688 (tt0) REVERT: A 14 GLU cc_start: 0.8401 (pm20) cc_final: 0.8047 (pm20) REVERT: A 62 TRP cc_start: 0.8027 (t-100) cc_final: 0.7490 (t-100) REVERT: D 46 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7816 (mm-30) REVERT: D 96 LYS cc_start: 0.8797 (tttt) cc_final: 0.8356 (tttt) REVERT: D 99 GLN cc_start: 0.7866 (tt0) cc_final: 0.7543 (pt0) REVERT: C 21 SER cc_start: 0.8782 (m) cc_final: 0.8083 (p) REVERT: C 55 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7839 (tt) REVERT: C 60 LEU cc_start: 0.9263 (mm) cc_final: 0.9007 (mt) REVERT: C 75 ASN cc_start: 0.7224 (m-40) cc_final: 0.6573 (m110) REVERT: F 28 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7862 (mmm160) REVERT: F 29 ASP cc_start: 0.8560 (m-30) cc_final: 0.8257 (m-30) REVERT: F 43 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7812 (mm-30) REVERT: F 66 MET cc_start: 0.7915 (mmm) cc_final: 0.7140 (mmm) REVERT: F 117 GLU cc_start: 0.5565 (tm-30) cc_final: 0.5319 (tm-30) REVERT: E 2 ASP cc_start: 0.8297 (t0) cc_final: 0.7984 (t0) REVERT: E 3 ILE cc_start: 0.9740 (mm) cc_final: 0.8622 (tt) REVERT: E 28 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8118 (tpp-160) REVERT: E 43 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 99 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8646 (mt0) REVERT: H 8 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6975 (tm-30) REVERT: H 70 THR cc_start: 0.8887 (m) cc_final: 0.8415 (p) REVERT: H 77 GLU cc_start: 0.7039 (mp0) cc_final: 0.6664 (mp0) REVERT: H 121 SER cc_start: 0.9487 (OUTLIER) cc_final: 0.9265 (t) REVERT: G 30 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8901 (mt) REVERT: G 39 ARG cc_start: 0.8370 (ttp-170) cc_final: 0.8091 (ttm170) REVERT: G 78 ASP cc_start: 0.8450 (t0) cc_final: 0.7622 (t0) REVERT: G 107 CYS cc_start: 0.9100 (m) cc_final: 0.8809 (m) REVERT: G 112 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8130 (ttm110) REVERT: G 121 SER cc_start: 0.8899 (t) cc_final: 0.8654 (t) REVERT: J 66 MET cc_start: 0.8280 (mmm) cc_final: 0.8023 (tpp) REVERT: J 141 SER cc_start: 0.9633 (m) cc_final: 0.9213 (p) REVERT: I 57 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: I 75 ASN cc_start: 0.7948 (m110) cc_final: 0.7645 (m110) REVERT: I 107 CYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8331 (t) REVERT: I 136 ASN cc_start: 0.8707 (p0) cc_final: 0.8467 (p0) REVERT: L 28 ARG cc_start: 0.8325 (mmm160) cc_final: 0.7320 (tpp-160) REVERT: L 39 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7881 (tpp80) REVERT: L 66 MET cc_start: 0.8118 (tpp) cc_final: 0.7764 (tpp) REVERT: L 117 GLU cc_start: 0.7259 (tp30) cc_final: 0.6901 (tp30) REVERT: K 6 TYR cc_start: 0.9004 (m-80) cc_final: 0.8393 (m-80) REVERT: K 66 MET cc_start: 0.7914 (mmp) cc_final: 0.7644 (mmp) REVERT: K 86 VAL cc_start: 0.8956 (t) cc_final: 0.8715 (p) REVERT: K 99 GLN cc_start: 0.8228 (mt0) cc_final: 0.7887 (mt0) REVERT: K 117 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: K 118 TYR cc_start: 0.9099 (t80) cc_final: 0.8201 (t80) outliers start: 83 outliers final: 64 residues processed: 473 average time/residue: 0.2548 time to fit residues: 173.5451 Evaluate side-chains 491 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 418 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 89 VAL 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 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 4 ASP Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 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 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 87 SER 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 12 THR 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 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 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 78 ASP Chi-restraints excluded: chain J residue 107 CYS Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 57 GLN Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 0.0050 chunk 143 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.114026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.096372 restraints weight = 23590.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098145 restraints weight = 17343.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099399 restraints weight = 14003.680| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14154 Z= 0.138 Angle : 0.670 11.976 19413 Z= 0.332 Chirality : 0.042 0.231 2211 Planarity : 0.005 0.068 2464 Dihedral : 4.173 59.821 1870 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 3.89 % Allowed : 25.28 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.21), residues: 1700 helix: 1.62 (0.15), residues: 1198 sheet: None (None), residues: 0 loop : 0.19 (0.30), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 62 HIS 0.004 0.001 HIS G 104 PHE 0.039 0.001 PHE K 110 TYR 0.019 0.002 TYR K 88 ARG 0.009 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 925) hydrogen bonds : angle 4.14367 ( 2712) SS BOND : bond 0.00862 ( 4) SS BOND : angle 1.36637 ( 8) covalent geometry : bond 0.00316 (14150) covalent geometry : angle 0.66966 (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: 59 poor density : 438 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6562 (t80) REVERT: B 31 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.7956 (mp) REVERT: B 38 TYR cc_start: 0.8723 (m-10) cc_final: 0.8459 (m-10) REVERT: B 66 MET cc_start: 0.8459 (mmm) cc_final: 0.8095 (mmm) REVERT: B 96 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8222 (ttmm) REVERT: B 99 GLN cc_start: 0.9260 (tt0) cc_final: 0.8705 (tt0) REVERT: A 14 GLU cc_start: 0.8451 (pm20) cc_final: 0.8089 (pm20) REVERT: A 62 TRP cc_start: 0.7967 (t-100) cc_final: 0.7454 (t-100) REVERT: D 46 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7834 (mm-30) REVERT: D 71 TRP cc_start: 0.8558 (t60) cc_final: 0.8288 (t60) REVERT: D 96 LYS cc_start: 0.8737 (tttt) cc_final: 0.8427 (tttt) REVERT: D 99 GLN cc_start: 0.7866 (tt0) cc_final: 0.7524 (pt0) REVERT: C 21 SER cc_start: 0.8674 (m) cc_final: 0.7973 (p) REVERT: C 55 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7983 (tt) REVERT: C 60 LEU cc_start: 0.9226 (mm) cc_final: 0.8966 (mt) REVERT: C 75 ASN cc_start: 0.7190 (m-40) cc_final: 0.6568 (m110) REVERT: C 90 ASN cc_start: 0.9105 (t0) cc_final: 0.8484 (t0) REVERT: F 28 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7830 (mmm160) REVERT: F 29 ASP cc_start: 0.8580 (m-30) cc_final: 0.8267 (m-30) REVERT: F 117 GLU cc_start: 0.5454 (tm-30) cc_final: 0.5236 (tm-30) REVERT: E 2 ASP cc_start: 0.8312 (t0) cc_final: 0.7961 (t0) REVERT: E 3 ILE cc_start: 0.9730 (mm) cc_final: 0.8642 (tt) REVERT: E 28 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8131 (tpp-160) REVERT: E 43 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7905 (mm-30) REVERT: E 99 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: H 8 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6870 (tm-30) REVERT: H 70 THR cc_start: 0.8833 (m) cc_final: 0.8359 (p) REVERT: H 77 GLU cc_start: 0.7021 (mp0) cc_final: 0.6640 (mp0) REVERT: H 121 SER cc_start: 0.9465 (m) cc_final: 0.9071 (t) REVERT: H 124 VAL cc_start: 0.9439 (OUTLIER) cc_final: 0.9131 (p) REVERT: G 30 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8864 (mt) REVERT: G 39 ARG cc_start: 0.8390 (ttp-170) cc_final: 0.7975 (ttm170) REVERT: G 107 CYS cc_start: 0.9061 (m) cc_final: 0.8782 (m) REVERT: G 112 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8097 (ttm110) REVERT: G 121 SER cc_start: 0.8911 (t) cc_final: 0.8660 (t) REVERT: J 141 SER cc_start: 0.9649 (m) cc_final: 0.9252 (p) REVERT: I 7 LYS cc_start: 0.9003 (tppp) cc_final: 0.8374 (tptp) REVERT: I 57 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: I 75 ASN cc_start: 0.7961 (m110) cc_final: 0.7634 (m110) REVERT: I 136 ASN cc_start: 0.8346 (p0) cc_final: 0.8120 (p0) REVERT: L 28 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7383 (tpp-160) REVERT: L 39 ARG cc_start: 0.8172 (tpp80) cc_final: 0.7787 (tpp80) REVERT: L 66 MET cc_start: 0.8265 (tpp) cc_final: 0.7922 (tpp) REVERT: L 117 GLU cc_start: 0.7190 (tp30) cc_final: 0.6878 (tp30) REVERT: K 6 TYR cc_start: 0.8960 (m-80) cc_final: 0.8323 (m-80) REVERT: K 86 VAL cc_start: 0.8954 (t) cc_final: 0.8686 (p) REVERT: K 99 GLN cc_start: 0.8214 (mt0) cc_final: 0.7848 (mt0) REVERT: K 117 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7133 (mp0) outliers start: 59 outliers final: 47 residues processed: 470 average time/residue: 0.2456 time to fit residues: 165.8132 Evaluate side-chains 474 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 418 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 89 VAL 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 F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 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 87 SER 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 124 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 78 ASP Chi-restraints excluded: chain J residue 89 VAL 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 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 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: 8.9990 chunk 135 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 I 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.091529 restraints weight = 23774.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.093366 restraints weight = 17334.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.094493 restraints weight = 13892.887| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14154 Z= 0.206 Angle : 0.736 11.612 19413 Z= 0.370 Chirality : 0.046 0.227 2211 Planarity : 0.005 0.066 2464 Dihedral : 4.332 57.283 1870 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 4.42 % Allowed : 25.54 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.21), residues: 1700 helix: 1.47 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : 0.08 (0.31), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 62 HIS 0.006 0.002 HIS K 104 PHE 0.028 0.002 PHE C 18 TYR 0.032 0.002 TYR K 118 ARG 0.010 0.001 ARG C 28 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 925) hydrogen bonds : angle 4.29888 ( 2712) SS BOND : bond 0.00925 ( 4) SS BOND : angle 1.59221 ( 8) covalent geometry : bond 0.00494 (14150) covalent geometry : angle 0.73529 (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 491 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 424 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.6549 (t80) REVERT: B 31 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8406 (mt) REVERT: B 38 TYR cc_start: 0.8868 (m-10) cc_final: 0.8543 (m-10) REVERT: B 83 ASP cc_start: 0.8433 (p0) cc_final: 0.8121 (p0) REVERT: B 96 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8153 (ttmm) REVERT: B 99 GLN cc_start: 0.9221 (tt0) cc_final: 0.8757 (tt0) REVERT: B 143 LEU cc_start: 0.8629 (tt) cc_final: 0.8346 (tt) REVERT: A 14 GLU cc_start: 0.8355 (pm20) cc_final: 0.8097 (pm20) REVERT: A 62 TRP cc_start: 0.8150 (t-100) cc_final: 0.7424 (t-100) REVERT: A 118 TYR cc_start: 0.9080 (t80) cc_final: 0.8840 (t80) REVERT: D 46 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7958 (mm-30) REVERT: D 61 CYS cc_start: 0.7019 (m) cc_final: 0.6716 (m) REVERT: C 21 SER cc_start: 0.8833 (m) cc_final: 0.8084 (p) REVERT: C 55 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7907 (tt) REVERT: C 75 ASN cc_start: 0.7259 (m-40) cc_final: 0.6623 (m110) REVERT: F 29 ASP cc_start: 0.8785 (m-30) cc_final: 0.8492 (m-30) REVERT: F 117 GLU cc_start: 0.5752 (tm-30) cc_final: 0.5425 (tm-30) REVERT: E 3 ILE cc_start: 0.9731 (mm) cc_final: 0.8681 (tt) REVERT: E 37 LEU cc_start: 0.8961 (tp) cc_final: 0.8728 (tp) REVERT: E 43 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7992 (mm-30) REVERT: E 99 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8503 (mt0) REVERT: H 8 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7300 (tm-30) REVERT: H 70 THR cc_start: 0.8943 (m) cc_final: 0.8464 (p) REVERT: H 77 GLU cc_start: 0.7091 (mp0) cc_final: 0.6748 (mp0) REVERT: G 30 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8797 (mt) REVERT: G 96 LYS cc_start: 0.7889 (tttt) cc_final: 0.7648 (ttpt) REVERT: G 107 CYS cc_start: 0.9145 (m) cc_final: 0.8925 (m) REVERT: G 112 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8219 (ttm110) REVERT: G 121 SER cc_start: 0.9014 (t) cc_final: 0.8702 (t) REVERT: J 141 SER cc_start: 0.9648 (m) cc_final: 0.9268 (p) REVERT: I 57 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: I 75 ASN cc_start: 0.8049 (m110) cc_final: 0.7436 (m110) REVERT: I 136 ASN cc_start: 0.8747 (p0) cc_final: 0.8516 (p0) REVERT: L 28 ARG cc_start: 0.8296 (mmm160) cc_final: 0.7386 (tpp-160) REVERT: L 39 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7998 (tpp80) REVERT: L 66 MET cc_start: 0.8371 (tpp) cc_final: 0.8052 (mpp) REVERT: L 117 GLU cc_start: 0.7403 (tp30) cc_final: 0.7179 (tp30) REVERT: K 1 MET cc_start: 0.7415 (tpp) cc_final: 0.6733 (tpp) REVERT: K 6 TYR cc_start: 0.9082 (m-80) cc_final: 0.8470 (m-80) REVERT: K 86 VAL cc_start: 0.8863 (t) cc_final: 0.8590 (p) REVERT: K 99 GLN cc_start: 0.8253 (mt0) cc_final: 0.7908 (mt0) REVERT: K 117 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7228 (mp0) outliers start: 67 outliers final: 52 residues processed: 462 average time/residue: 0.2503 time to fit residues: 166.2800 Evaluate side-chains 474 residues out of total 1515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 415 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain A residue 8 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 87 SER Chi-restraints excluded: chain A residue 89 VAL 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 F residue 16 LEU Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 72 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 44 SER Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 89 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 8 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 129 optimal weight: 0.0270 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7642 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.114489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.096669 restraints weight = 23369.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.098556 restraints weight = 16881.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.099860 restraints weight = 13380.568| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14154 Z= 0.138 Angle : 0.699 11.884 19413 Z= 0.343 Chirality : 0.042 0.237 2211 Planarity : 0.005 0.064 2464 Dihedral : 4.072 45.787 1870 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.17 % Allowed : 27.00 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.21), residues: 1700 helix: 1.61 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : 0.16 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 62 HIS 0.004 0.001 HIS J 104 PHE 0.025 0.001 PHE A 23 TYR 0.024 0.002 TYR K 118 ARG 0.010 0.001 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 925) hydrogen bonds : angle 4.15300 ( 2712) SS BOND : bond 0.00852 ( 4) SS BOND : angle 1.31762 ( 8) covalent geometry : bond 0.00304 (14150) covalent geometry : angle 0.69846 (19405) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.43 seconds wall clock time: 89 minutes 27.17 seconds (5367.17 seconds total)