Starting phenix.real_space_refine on Thu Sep 18 08:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cjz_45637/09_2025/9cjz_45637.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cjz_45637/09_2025/9cjz_45637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cjz_45637/09_2025/9cjz_45637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cjz_45637/09_2025/9cjz_45637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cjz_45637/09_2025/9cjz_45637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cjz_45637/09_2025/9cjz_45637.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 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 63 5.16 5 C 9779 2.51 5 N 2616 2.21 5 O 2971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15429 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2300 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 19, 'TRANS': 271} Chain breaks: 4 Chain: "B" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain: "C" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2311 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 20, 'TRANS': 272} Chain breaks: 4 Chain: "D" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain: "E" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2315 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 20, 'TRANS': 272} Chain breaks: 4 Chain: "F" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1324 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 1, 'TRANS': 160} Chain: "H" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "J" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "K" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 646 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain breaks: 2 Chain: "L" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 677 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain breaks: 2 Chain: "M" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Chain: "N" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 685 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain breaks: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.25 Number of scatterers: 15429 At special positions: 0 Unit cell: (118.77, 128.76, 152.07, 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 63 16.00 O 2971 8.00 N 2616 7.00 C 9779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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: 1.31 Conformation dependent library (CDL) restraints added in 742.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3610 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 44 sheets defined 17.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 76 through 79A removed outlier: 3.777A pdb=" N LEU A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 79A" --> pdb=" O GLU A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79A' Processing helix chain 'A' and resid 110 through 114 removed outlier: 3.631A pdb=" N SER A 114 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 57 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 74 through 125 removed outlier: 3.631A pdb=" N PHE B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 removed outlier: 4.115A pdb=" N MET B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 164 removed outlier: 3.937A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 76 through 79A removed outlier: 3.847A pdb=" N LEU C 79 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE C 79A" --> pdb=" O GLU C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 79A' Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'D' and resid 37 through 57 removed outlier: 3.523A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 74 through 126 removed outlier: 3.725A pdb=" N LEU D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.906A pdb=" N GLU D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 76 through 79A removed outlier: 3.885A pdb=" N LEU E 79 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 79A" --> pdb=" O GLU E 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 79A' Processing helix chain 'F' and resid 38 through 57 Processing helix chain 'F' and resid 71 through 73 No H-bonds generated for 'chain 'F' and resid 71 through 73' Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.849A pdb=" N LEU F 108 " --> pdb=" O ASN F 104 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 removed outlier: 4.127A pdb=" N MET F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 150 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 164 removed outlier: 3.561A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.026A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.720A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.173A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.825A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 4.118A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.767A pdb=" N CYS B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 139 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.736A pdb=" N GLU A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.462A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117B through 118 removed outlier: 3.810A pdb=" N ALA A 259 " --> pdb=" O GLU A 117B" (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.789A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 146 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 151 through 152 removed outlier: 3.708A pdb=" N ALA A 253 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.193A pdb=" N LYS A 166 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 176 through 184 removed outlier: 3.684A pdb=" N LEU A 237 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.634A pdb=" N TYR A 209 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 35 through 36 removed outlier: 3.561A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS D 137 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 139 " --> pdb=" O LYS D 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.519A pdb=" N THR C 28 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS C 32 " --> pdb=" O THR C 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.858A pdb=" N GLU C 44 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.642A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 117B through 118 removed outlier: 3.922A pdb=" N ALA C 259 " --> pdb=" O GLU C 117B" (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 118 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.849A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 184 removed outlier: 3.676A pdb=" N LEU C 237 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 205 through 206 removed outlier: 3.915A pdb=" N TYR C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC4, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC5, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.945A pdb=" N GLU E 44 " --> pdb=" O PHE E 294 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.678A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 117B through 118 removed outlier: 3.865A pdb=" N ALA E 259 " --> pdb=" O GLU E 117B" (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 118 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.835A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 151 through 152 removed outlier: 3.675A pdb=" N ALA E 253 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 176 through 184 removed outlier: 3.524A pdb=" N ASN E 231 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS E 184 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG E 229 " --> pdb=" O HIS E 184 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 205 through 206 removed outlier: 3.692A pdb=" N TYR E 209 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.056A pdb=" N TYR H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 57 through 59 removed outlier: 4.056A pdb=" N TYR H 50 " --> pdb=" O TYR H 58 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.606A pdb=" N THR J 68 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 57 through 59 removed outlier: 4.177A pdb=" N TYR J 50 " --> pdb=" O TYR J 58 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 48 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 57 through 59 removed outlier: 4.177A pdb=" N TYR J 50 " --> pdb=" O TYR J 58 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 48 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL J 102 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.503A pdb=" N THR K 5 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG K 24 " --> pdb=" O THR K 5 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.548A pdb=" N GLN K 37 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.601A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 45 through 49 removed outlier: 3.524A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN L 38 " --> pdb=" O VAL L 85 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.179A pdb=" N TYR M 50 " --> pdb=" O TYR M 58 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA M 93 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL M 102 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.179A pdb=" N TYR M 50 " --> pdb=" O TYR M 58 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE8, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.626A pdb=" N GLN N 37 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLN N 89 " --> pdb=" O ALA N 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN N 38 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN N 90 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4962 1.34 - 1.46: 3786 1.46 - 1.58: 6964 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 15796 Sorted by residual: bond pdb=" N PHE B 9 " pdb=" CA PHE B 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N VAL M 2 " pdb=" CA VAL M 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N PHE F 9 " pdb=" CA PHE F 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" N ASP E 11 " pdb=" CA ASP E 11 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N PHE D 9 " pdb=" CA PHE D 9 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 15791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 20941 1.52 - 3.04: 384 3.04 - 4.56: 91 4.56 - 6.08: 7 6.08 - 7.61: 5 Bond angle restraints: 21428 Sorted by residual: angle pdb=" CA MET D 17 " pdb=" CB MET D 17 " pdb=" CG MET D 17 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.30e+00 angle pdb=" C TRP N 94 " pdb=" CA TRP N 94 " pdb=" CB TRP N 94 " ideal model delta sigma weight residual 113.57 109.38 4.19 1.57e+00 4.06e-01 7.13e+00 angle pdb=" CB MET D 17 " pdb=" CG MET D 17 " pdb=" SD MET D 17 " ideal model delta sigma weight residual 112.70 120.31 -7.61 3.00e+00 1.11e-01 6.43e+00 angle pdb=" CA GLU B 120 " pdb=" CB GLU B 120 " pdb=" CG GLU B 120 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" N ILE J 55 " pdb=" CA ILE J 55 " pdb=" C ILE J 55 " ideal model delta sigma weight residual 111.48 109.30 2.18 9.40e-01 1.13e+00 5.38e+00 ... (remaining 21423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8071 17.97 - 35.95: 941 35.95 - 53.92: 267 53.92 - 71.90: 45 71.90 - 89.87: 17 Dihedral angle restraints: 9341 sinusoidal: 3702 harmonic: 5639 Sorted by residual: dihedral pdb=" CA ASN L 93 " pdb=" C ASN L 93 " pdb=" N TRP L 94 " pdb=" CA TRP L 94 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ASN N 93 " pdb=" C ASN N 93 " pdb=" N TRP N 94 " pdb=" CA TRP N 94 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA ASN K 93 " pdb=" C ASN K 93 " pdb=" N TRP K 94 " pdb=" CA TRP K 94 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 9338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1435 0.028 - 0.055: 604 0.055 - 0.083: 119 0.083 - 0.110: 120 0.110 - 0.138: 44 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CA ILE L 2 " pdb=" N ILE L 2 " pdb=" C ILE L 2 " pdb=" CB ILE L 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE K 2 " pdb=" N ILE K 2 " pdb=" C ILE K 2 " pdb=" CB ILE K 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE N 2 " pdb=" N ILE N 2 " pdb=" C ILE N 2 " pdb=" CB ILE N 2 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2319 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 106 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C GLU C 106 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU C 106 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU C 107 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 10 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.96e+00 pdb=" C ILE D 10 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE D 10 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU D 11 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 17 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C MET D 17 " -0.023 2.00e-02 2.50e+03 pdb=" O MET D 17 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL D 18 " 0.008 2.00e-02 2.50e+03 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 194 2.49 - 3.10: 12349 3.10 - 3.70: 23302 3.70 - 4.30: 30871 4.30 - 4.90: 50806 Nonbonded interactions: 117522 Sorted by model distance: nonbonded pdb=" OG1 THR C 131 " pdb=" OG1 THR C 155 " model vdw 1.892 3.040 nonbonded pdb=" OE1 GLN B 27 " pdb=" OH TYR H 58 " model vdw 1.912 3.040 nonbonded pdb=" OE1 GLN D 27 " pdb=" OH TYR J 58 " model vdw 1.912 3.040 nonbonded pdb=" OE1 GLN F 27 " pdb=" OH TYR M 58 " model vdw 1.929 3.040 nonbonded pdb=" O TYR A 168 " pdb=" OG1 THR A 242 " model vdw 1.967 3.040 ... (remaining 117517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 261 or resid 266 through 325)) selection = (chain 'C' and (resid 11 through 154 or resid 161 through 185 or resid 200 throu \ gh 325)) selection = (chain 'E' and (resid 11 through 185 or resid 200 through 261 or resid 266 throu \ gh 325)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 2 through 7 or resid 19 through 104)) selection = (chain 'N' and (resid 2 through 7 or resid 19 through 75 or resid 83 through 104 \ )) } 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: 4.640 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.660 Find NCS groups from input model: 0.360 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:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15814 Z= 0.146 Angle : 0.542 7.605 21464 Z= 0.287 Chirality : 0.039 0.138 2322 Planarity : 0.003 0.026 2742 Dihedral : 16.723 89.870 5677 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.12 % Allowed : 25.75 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.19), residues: 1891 helix: 1.69 (0.31), residues: 275 sheet: -1.99 (0.29), residues: 333 loop : -2.15 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 106 TYR 0.007 0.001 TYR E 105 PHE 0.008 0.001 PHE F 140 TRP 0.011 0.001 TRP E 153 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00304 (15796) covalent geometry : angle 0.54191 (21428) SS BOND : bond 0.00275 ( 18) SS BOND : angle 0.66305 ( 36) hydrogen bonds : bond 0.22534 ( 405) hydrogen bonds : angle 8.07454 ( 1104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 412 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8040 (t0) cc_final: 0.7694 (m-40) REVERT: A 149 ARG cc_start: 0.6433 (mmm160) cc_final: 0.6160 (mmt-90) REVERT: B 76 ARG cc_start: 0.6790 (tpp80) cc_final: 0.6238 (mtt-85) REVERT: B 77 MET cc_start: 0.7132 (mmm) cc_final: 0.6121 (mtt) REVERT: B 168 LEU cc_start: 0.7986 (tp) cc_final: 0.7573 (tp) REVERT: B 170 ARG cc_start: 0.7776 (mtm180) cc_final: 0.6289 (mmp80) REVERT: C 17 TYR cc_start: 0.6366 (p90) cc_final: 0.5940 (p90) REVERT: C 44 GLU cc_start: 0.6029 (pt0) cc_final: 0.5456 (tm-30) REVERT: C 45 ASP cc_start: 0.6330 (m-30) cc_final: 0.5943 (m-30) REVERT: C 209 TYR cc_start: 0.6509 (t80) cc_final: 0.6082 (t80) REVERT: C 295 GLN cc_start: 0.6917 (pt0) cc_final: 0.6674 (pt0) REVERT: C 310 ARG cc_start: 0.6974 (ttp-110) cc_final: 0.6676 (ttp-110) REVERT: D 46 ASN cc_start: 0.7929 (t0) cc_final: 0.7561 (t0) REVERT: D 149 MET cc_start: 0.6778 (mmp) cc_final: 0.6552 (mmp) REVERT: E 172 LYS cc_start: 0.5146 (ttmt) cc_final: 0.4872 (mtmm) REVERT: E 229 ARG cc_start: 0.4953 (mtm-85) cc_final: 0.4676 (mtm-85) REVERT: F 24 TYR cc_start: 0.7564 (m-80) cc_final: 0.7044 (m-80) REVERT: F 138 PHE cc_start: 0.6300 (m-80) cc_final: 0.5866 (m-80) REVERT: H 38 ARG cc_start: 0.6161 (ptm160) cc_final: 0.5850 (ptm160) REVERT: J 28 THR cc_start: 0.7187 (m) cc_final: 0.6961 (p) REVERT: K 42 GLN cc_start: 0.7466 (pt0) cc_final: 0.7097 (pt0) REVERT: K 71 PHE cc_start: 0.7541 (m-80) cc_final: 0.7251 (m-80) REVERT: K 103 LYS cc_start: 0.8443 (ptmm) cc_final: 0.7341 (mmmt) REVERT: L 38 GLN cc_start: 0.7738 (pp30) cc_final: 0.7267 (pp30) REVERT: M 55 ILE cc_start: 0.7696 (mm) cc_final: 0.7386 (mt) REVERT: N 24 ARG cc_start: 0.6229 (ttm-80) cc_final: 0.5677 (ttm-80) REVERT: N 33 LEU cc_start: 0.7073 (tt) cc_final: 0.6685 (tt) REVERT: N 37 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7970 (tm-30) outliers start: 2 outliers final: 0 residues processed: 413 average time/residue: 0.1275 time to fit residues: 77.0918 Evaluate side-chains 273 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 183 HIS D 60 ASN E 295 GLN ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.188596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.166883 restraints weight = 23330.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167331 restraints weight = 20385.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167925 restraints weight = 18524.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.168021 restraints weight = 16839.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.168184 restraints weight = 16771.187| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15814 Z= 0.142 Angle : 0.671 9.196 21464 Z= 0.347 Chirality : 0.044 0.151 2322 Planarity : 0.005 0.077 2742 Dihedral : 4.471 21.649 2099 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.86 % Allowed : 27.62 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.19), residues: 1891 helix: 1.77 (0.32), residues: 277 sheet: -1.86 (0.28), residues: 340 loop : -1.98 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 75 TYR 0.013 0.001 TYR M 50 PHE 0.020 0.002 PHE M 29 TRP 0.021 0.002 TRP E 153 HIS 0.005 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00320 (15796) covalent geometry : angle 0.67046 (21428) SS BOND : bond 0.00563 ( 18) SS BOND : angle 0.94176 ( 36) hydrogen bonds : bond 0.05049 ( 405) hydrogen bonds : angle 5.95376 ( 1104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.6065 (mt-10) REVERT: B 77 MET cc_start: 0.8003 (mmm) cc_final: 0.7237 (mtt) REVERT: B 149 MET cc_start: 0.6089 (mmp) cc_final: 0.5799 (mmp) REVERT: B 170 ARG cc_start: 0.6021 (mtm180) cc_final: 0.5023 (mmp80) REVERT: C 27 ASP cc_start: 0.5489 (m-30) cc_final: 0.5281 (m-30) REVERT: C 298 HIS cc_start: 0.6665 (t-90) cc_final: 0.6429 (t-170) REVERT: D 46 ASN cc_start: 0.7402 (t0) cc_final: 0.7120 (t0) REVERT: D 63 PHE cc_start: 0.5887 (m-10) cc_final: 0.5564 (m-80) REVERT: D 77 MET cc_start: 0.7958 (mmt) cc_final: 0.7753 (mmt) REVERT: J 28 THR cc_start: 0.7809 (m) cc_final: 0.7541 (p) REVERT: K 42 GLN cc_start: 0.8221 (pt0) cc_final: 0.7973 (pt0) REVERT: K 91 ASP cc_start: 0.6782 (m-30) cc_final: 0.5733 (m-30) REVERT: K 94 TRP cc_start: 0.7805 (t-100) cc_final: 0.7231 (t-100) REVERT: K 103 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7271 (mmmt) REVERT: L 54 ARG cc_start: 0.7230 (mmm160) cc_final: 0.6239 (mmt-90) REVERT: L 60 ASP cc_start: 0.7204 (t0) cc_final: 0.6952 (t0) REVERT: M 43 LYS cc_start: 0.7290 (ptmm) cc_final: 0.6594 (pttm) REVERT: M 55 ILE cc_start: 0.7992 (mm) cc_final: 0.7614 (mt) REVERT: N 91 ASP cc_start: 0.6965 (m-30) cc_final: 0.6081 (m-30) REVERT: N 94 TRP cc_start: 0.7782 (t-100) cc_final: 0.7391 (t-100) outliers start: 66 outliers final: 35 residues processed: 366 average time/residue: 0.1141 time to fit residues: 62.6199 Evaluate side-chains 303 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 77 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 162 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 0.0370 chunk 6 optimal weight: 0.0570 chunk 147 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN C 183 HIS ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 HIS ** E 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS K 38 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.188070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.167882 restraints weight = 23785.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167816 restraints weight = 22662.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168359 restraints weight = 20911.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168626 restraints weight = 18830.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168772 restraints weight = 17657.484| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15814 Z= 0.122 Angle : 0.601 7.697 21464 Z= 0.312 Chirality : 0.043 0.156 2322 Planarity : 0.004 0.080 2742 Dihedral : 4.328 20.333 2099 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.56 % Allowed : 28.09 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.19), residues: 1891 helix: 1.97 (0.33), residues: 277 sheet: -1.25 (0.29), residues: 314 loop : -2.00 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 310 TYR 0.010 0.001 TYR H 59 PHE 0.017 0.001 PHE M 67 TRP 0.018 0.001 TRP A 127 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00267 (15796) covalent geometry : angle 0.60049 (21428) SS BOND : bond 0.00417 ( 18) SS BOND : angle 0.89707 ( 36) hydrogen bonds : bond 0.04567 ( 405) hydrogen bonds : angle 5.49823 ( 1104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 319 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6211 (tpp) REVERT: B 77 MET cc_start: 0.7998 (mmm) cc_final: 0.7324 (mtt) REVERT: B 170 ARG cc_start: 0.6063 (mtm180) cc_final: 0.4843 (mmp80) REVERT: C 101 TYR cc_start: 0.5482 (OUTLIER) cc_final: 0.4493 (t80) REVERT: C 298 HIS cc_start: 0.6561 (t-90) cc_final: 0.6344 (t-170) REVERT: C 308 TYR cc_start: 0.7241 (t80) cc_final: 0.7038 (t80) REVERT: D 46 ASN cc_start: 0.7474 (t0) cc_final: 0.7202 (t0) REVERT: D 63 PHE cc_start: 0.5843 (m-10) cc_final: 0.5508 (m-80) REVERT: D 77 MET cc_start: 0.7848 (mmt) cc_final: 0.7289 (mmt) REVERT: D 109 ASP cc_start: 0.7110 (m-30) cc_final: 0.6807 (t70) REVERT: E 107 GLU cc_start: 0.6648 (mp0) cc_final: 0.6416 (mp0) REVERT: E 119 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6221 (tt0) REVERT: E 295 GLN cc_start: 0.6597 (pt0) cc_final: 0.6152 (pt0) REVERT: F 77 MET cc_start: 0.7949 (mmm) cc_final: 0.7256 (mtt) REVERT: J 28 THR cc_start: 0.7774 (m) cc_final: 0.7503 (p) REVERT: J 29 PHE cc_start: 0.8137 (t80) cc_final: 0.7924 (t80) REVERT: K 42 GLN cc_start: 0.8302 (pt0) cc_final: 0.8002 (pt0) REVERT: K 91 ASP cc_start: 0.6957 (m-30) cc_final: 0.5777 (m-30) REVERT: K 94 TRP cc_start: 0.7874 (t-100) cc_final: 0.7381 (t-100) REVERT: K 103 LYS cc_start: 0.7756 (ptmm) cc_final: 0.7200 (mmmt) REVERT: L 54 ARG cc_start: 0.7224 (mmm160) cc_final: 0.6193 (mmt-90) REVERT: L 60 ASP cc_start: 0.7465 (t70) cc_final: 0.7132 (t0) REVERT: M 43 LYS cc_start: 0.7343 (ptmm) cc_final: 0.6616 (pttp) REVERT: M 55 ILE cc_start: 0.8046 (mm) cc_final: 0.7642 (mt) REVERT: N 91 ASP cc_start: 0.6925 (m-30) cc_final: 0.6514 (m-30) REVERT: N 94 TRP cc_start: 0.7795 (t-100) cc_final: 0.7470 (t-100) outliers start: 78 outliers final: 41 residues processed: 366 average time/residue: 0.1094 time to fit residues: 61.1823 Evaluate side-chains 328 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 250 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 25 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 185 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 184 HIS C 47 HIS C 183 HIS C 231 ASN D 47 GLN E 250 ASN F 42 GLN K 38 GLN N 38 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.189161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.164669 restraints weight = 27114.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.166028 restraints weight = 22571.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.166501 restraints weight = 19847.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.167404 restraints weight = 17371.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.167605 restraints weight = 15552.804| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15814 Z= 0.142 Angle : 0.622 7.843 21464 Z= 0.322 Chirality : 0.043 0.154 2322 Planarity : 0.005 0.085 2742 Dihedral : 4.419 20.974 2099 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.32 % Allowed : 28.38 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.19), residues: 1891 helix: 1.96 (0.33), residues: 277 sheet: -1.36 (0.29), residues: 332 loop : -2.01 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 229 TYR 0.011 0.001 TYR M 50 PHE 0.032 0.002 PHE H 67 TRP 0.026 0.001 TRP A 127 HIS 0.005 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00329 (15796) covalent geometry : angle 0.62141 (21428) SS BOND : bond 0.00444 ( 18) SS BOND : angle 1.07703 ( 36) hydrogen bonds : bond 0.04619 ( 405) hydrogen bonds : angle 5.42898 ( 1104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 299 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASN cc_start: 0.5202 (OUTLIER) cc_final: 0.4929 (m-40) REVERT: A 274 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6413 (tpp) REVERT: B 77 MET cc_start: 0.8082 (mmm) cc_final: 0.7527 (mtt) REVERT: C 101 TYR cc_start: 0.5332 (OUTLIER) cc_final: 0.4319 (t80) REVERT: C 231 ASN cc_start: 0.5680 (OUTLIER) cc_final: 0.5437 (p0) REVERT: D 46 ASN cc_start: 0.7724 (t0) cc_final: 0.7458 (t0) REVERT: D 63 PHE cc_start: 0.6039 (m-10) cc_final: 0.5688 (m-80) REVERT: D 77 MET cc_start: 0.7915 (mmt) cc_final: 0.7338 (mmm) REVERT: D 109 ASP cc_start: 0.7394 (m-30) cc_final: 0.7031 (t70) REVERT: E 119 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6271 (tt0) REVERT: E 237 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6241 (pt) REVERT: E 295 GLN cc_start: 0.6401 (pt0) cc_final: 0.5789 (pt0) REVERT: F 24 TYR cc_start: 0.8063 (m-80) cc_final: 0.7805 (m-80) REVERT: F 77 MET cc_start: 0.8367 (mmm) cc_final: 0.7249 (mtt) REVERT: K 42 GLN cc_start: 0.8365 (pt0) cc_final: 0.8060 (pt0) REVERT: K 91 ASP cc_start: 0.7120 (m-30) cc_final: 0.6059 (m-30) REVERT: K 94 TRP cc_start: 0.8022 (t-100) cc_final: 0.7678 (t-100) REVERT: K 103 LYS cc_start: 0.7972 (ptmm) cc_final: 0.7345 (mmmt) REVERT: L 54 ARG cc_start: 0.7324 (mmm160) cc_final: 0.6202 (mmt-90) REVERT: L 60 ASP cc_start: 0.7678 (t70) cc_final: 0.7321 (t0) REVERT: M 43 LYS cc_start: 0.7569 (ptmm) cc_final: 0.6844 (pttp) REVERT: N 21 LEU cc_start: 0.7869 (tt) cc_final: 0.6982 (mp) REVERT: N 91 ASP cc_start: 0.7403 (m-30) cc_final: 0.6746 (m-30) REVERT: N 94 TRP cc_start: 0.7935 (t-100) cc_final: 0.7619 (t-100) outliers start: 91 outliers final: 61 residues processed: 357 average time/residue: 0.1083 time to fit residues: 59.9313 Evaluate side-chains 343 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 140 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.0040 chunk 117 optimal weight: 0.0870 chunk 171 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 overall best weight: 0.2770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 184 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 250 ASN C 298 HIS ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.192667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.167214 restraints weight = 26990.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169954 restraints weight = 19963.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.171868 restraints weight = 16033.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173024 restraints weight = 13677.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.174186 restraints weight = 12230.964| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15814 Z= 0.109 Angle : 0.600 11.936 21464 Z= 0.304 Chirality : 0.042 0.316 2322 Planarity : 0.005 0.084 2742 Dihedral : 4.249 19.820 2099 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.33 % Allowed : 29.72 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.19), residues: 1891 helix: 2.02 (0.33), residues: 277 sheet: -1.02 (0.30), residues: 326 loop : -1.90 (0.16), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 310 TYR 0.013 0.001 TYR E 105 PHE 0.025 0.001 PHE H 67 TRP 0.023 0.001 TRP A 127 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00241 (15796) covalent geometry : angle 0.59956 (21428) SS BOND : bond 0.00307 ( 18) SS BOND : angle 0.77037 ( 36) hydrogen bonds : bond 0.04146 ( 405) hydrogen bonds : angle 5.15104 ( 1104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 301 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6517 (pt) REVERT: A 241 ASP cc_start: 0.7098 (m-30) cc_final: 0.6870 (p0) REVERT: A 250 ASN cc_start: 0.5582 (OUTLIER) cc_final: 0.5348 (m-40) REVERT: A 274 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6351 (tpp) REVERT: A 295 GLN cc_start: 0.6649 (pt0) cc_final: 0.6224 (pt0) REVERT: B 77 MET cc_start: 0.7944 (mmm) cc_final: 0.7240 (mtt) REVERT: C 101 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.4314 (t80) REVERT: C 209 TYR cc_start: 0.7193 (t80) cc_final: 0.6751 (t80) REVERT: D 10 ILE cc_start: 0.7486 (pt) cc_final: 0.7282 (pt) REVERT: D 46 ASN cc_start: 0.7622 (t0) cc_final: 0.7256 (t0) REVERT: D 63 PHE cc_start: 0.6152 (m-10) cc_final: 0.5808 (m-80) REVERT: D 77 MET cc_start: 0.7727 (mmt) cc_final: 0.7455 (mmm) REVERT: E 104 ASP cc_start: 0.7827 (p0) cc_final: 0.7409 (p0) REVERT: E 295 GLN cc_start: 0.6761 (pt0) cc_final: 0.6183 (pt0) REVERT: F 24 TYR cc_start: 0.7858 (m-80) cc_final: 0.7620 (m-80) REVERT: F 77 MET cc_start: 0.8029 (mmm) cc_final: 0.7488 (mtt) REVERT: H 29 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7178 (t80) REVERT: H 35 SER cc_start: 0.8473 (t) cc_final: 0.8268 (m) REVERT: K 42 GLN cc_start: 0.8354 (pt0) cc_final: 0.8045 (pt0) REVERT: K 91 ASP cc_start: 0.7257 (m-30) cc_final: 0.6186 (m-30) REVERT: K 94 TRP cc_start: 0.7995 (t-100) cc_final: 0.7680 (t-100) REVERT: K 103 LYS cc_start: 0.7889 (ptmm) cc_final: 0.7305 (mmmt) REVERT: L 54 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6185 (mmt-90) REVERT: L 60 ASP cc_start: 0.7569 (t70) cc_final: 0.7209 (t0) REVERT: M 43 LYS cc_start: 0.7539 (ptmm) cc_final: 0.6877 (pttp) REVERT: N 21 LEU cc_start: 0.7812 (tt) cc_final: 0.6976 (mp) REVERT: N 91 ASP cc_start: 0.7308 (m-30) cc_final: 0.6404 (m-30) outliers start: 74 outliers final: 52 residues processed: 349 average time/residue: 0.1060 time to fit residues: 57.5788 Evaluate side-chains 330 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain N residue 3 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 132 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 96 optimal weight: 0.0070 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 0.0030 chunk 136 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 183 HIS A 184 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 42 GLN F 43 ASN J 39 GLN K 37 GLN K 38 GLN N 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.191595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.165843 restraints weight = 26811.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168483 restraints weight = 19944.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.170364 restraints weight = 16092.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.171723 restraints weight = 13806.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.172677 restraints weight = 12301.086| |-----------------------------------------------------------------------------| r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15814 Z= 0.115 Angle : 0.597 9.741 21464 Z= 0.303 Chirality : 0.042 0.174 2322 Planarity : 0.005 0.086 2742 Dihedral : 4.187 20.033 2099 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.97 % Allowed : 29.20 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.19), residues: 1891 helix: 2.05 (0.33), residues: 277 sheet: -0.96 (0.29), residues: 332 loop : -1.88 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 310 TYR 0.012 0.001 TYR E 105 PHE 0.018 0.001 PHE H 67 TRP 0.023 0.001 TRP A 127 HIS 0.004 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00262 (15796) covalent geometry : angle 0.59655 (21428) SS BOND : bond 0.00303 ( 18) SS BOND : angle 0.72582 ( 36) hydrogen bonds : bond 0.04124 ( 405) hydrogen bonds : angle 5.06705 ( 1104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 286 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6504 (pt) REVERT: A 274 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.6245 (tpp) REVERT: B 77 MET cc_start: 0.7917 (mmm) cc_final: 0.7347 (mtt) REVERT: C 101 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.4311 (t80) REVERT: C 209 TYR cc_start: 0.7241 (t80) cc_final: 0.6859 (t80) REVERT: D 46 ASN cc_start: 0.7631 (t0) cc_final: 0.7312 (t0) REVERT: D 63 PHE cc_start: 0.6104 (m-10) cc_final: 0.5784 (m-80) REVERT: D 77 MET cc_start: 0.7740 (mmt) cc_final: 0.7055 (mmm) REVERT: E 104 ASP cc_start: 0.7876 (p0) cc_final: 0.7593 (p0) REVERT: E 250 ASN cc_start: 0.5148 (OUTLIER) cc_final: 0.4530 (m110) REVERT: E 295 GLN cc_start: 0.6823 (pt0) cc_final: 0.6285 (pt0) REVERT: F 24 TYR cc_start: 0.7919 (m-80) cc_final: 0.7699 (m-80) REVERT: F 77 MET cc_start: 0.8142 (mmm) cc_final: 0.7602 (mtt) REVERT: H 29 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7175 (t80) REVERT: H 35 SER cc_start: 0.8543 (t) cc_final: 0.8307 (m) REVERT: J 29 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7525 (t80) REVERT: K 42 GLN cc_start: 0.8314 (pt0) cc_final: 0.8061 (pt0) REVERT: K 91 ASP cc_start: 0.7279 (m-30) cc_final: 0.6318 (m-30) REVERT: K 94 TRP cc_start: 0.8006 (t-100) cc_final: 0.7789 (t-100) REVERT: K 103 LYS cc_start: 0.7889 (ptmm) cc_final: 0.7259 (mmmt) REVERT: L 54 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6317 (mmt-90) REVERT: L 60 ASP cc_start: 0.7622 (t70) cc_final: 0.7287 (t0) REVERT: M 35 SER cc_start: 0.8630 (t) cc_final: 0.8364 (m) REVERT: M 43 LYS cc_start: 0.7487 (ptmm) cc_final: 0.7175 (pttm) REVERT: N 21 LEU cc_start: 0.7808 (tt) cc_final: 0.7053 (mp) outliers start: 85 outliers final: 64 residues processed: 342 average time/residue: 0.1040 time to fit residues: 55.7256 Evaluate side-chains 340 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.0870 chunk 2 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 42 GLN F 43 ASN H 39 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.187457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.163997 restraints weight = 26853.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.163864 restraints weight = 24214.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.165042 restraints weight = 24483.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165628 restraints weight = 19876.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.166180 restraints weight = 17828.449| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15814 Z= 0.159 Angle : 0.635 10.268 21464 Z= 0.327 Chirality : 0.043 0.175 2322 Planarity : 0.005 0.095 2742 Dihedral : 4.413 20.494 2099 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.79 % Allowed : 28.73 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.19), residues: 1891 helix: 1.93 (0.33), residues: 277 sheet: -1.04 (0.29), residues: 342 loop : -1.99 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 310 TYR 0.014 0.001 TYR E 105 PHE 0.025 0.002 PHE H 67 TRP 0.027 0.002 TRP A 127 HIS 0.007 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00372 (15796) covalent geometry : angle 0.63447 (21428) SS BOND : bond 0.00386 ( 18) SS BOND : angle 0.86368 ( 36) hydrogen bonds : bond 0.04582 ( 405) hydrogen bonds : angle 5.18887 ( 1104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 277 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.5313 (tm-30) REVERT: A 237 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6349 (pt) REVERT: A 274 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6204 (tpp) REVERT: B 77 MET cc_start: 0.7926 (mmm) cc_final: 0.7369 (mtt) REVERT: C 101 TYR cc_start: 0.5678 (OUTLIER) cc_final: 0.4526 (t80) REVERT: D 46 ASN cc_start: 0.7851 (t0) cc_final: 0.7528 (t0) REVERT: D 63 PHE cc_start: 0.6178 (m-10) cc_final: 0.5930 (m-80) REVERT: D 77 MET cc_start: 0.7812 (mmt) cc_final: 0.7175 (mmm) REVERT: E 69 TRP cc_start: 0.7923 (OUTLIER) cc_final: 0.6880 (t-100) REVERT: E 104 ASP cc_start: 0.7969 (p0) cc_final: 0.7571 (p0) REVERT: E 119 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6641 (tt0) REVERT: E 250 ASN cc_start: 0.5376 (OUTLIER) cc_final: 0.4749 (m110) REVERT: F 24 TYR cc_start: 0.8021 (m-80) cc_final: 0.7806 (m-80) REVERT: F 77 MET cc_start: 0.8131 (mmm) cc_final: 0.7453 (mtt) REVERT: H 29 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7453 (t80) REVERT: H 35 SER cc_start: 0.8643 (t) cc_final: 0.8355 (m) REVERT: J 29 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7444 (t80) REVERT: K 42 GLN cc_start: 0.8324 (pt0) cc_final: 0.8075 (pt0) REVERT: K 103 LYS cc_start: 0.7976 (ptmm) cc_final: 0.7294 (mmmt) REVERT: M 43 LYS cc_start: 0.7584 (ptmm) cc_final: 0.7258 (pttm) REVERT: N 21 LEU cc_start: 0.7902 (tt) cc_final: 0.7100 (mp) outliers start: 99 outliers final: 79 residues processed: 340 average time/residue: 0.1040 time to fit residues: 55.2029 Evaluate side-chains 353 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 265 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 148 CYS Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 139 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 181 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 184 HIS A 250 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 42 GLN H 39 GLN J 39 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.188924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.165283 restraints weight = 26848.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.165392 restraints weight = 20865.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166205 restraints weight = 19943.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167253 restraints weight = 17458.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.167878 restraints weight = 15444.848| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15814 Z= 0.116 Angle : 0.608 10.826 21464 Z= 0.309 Chirality : 0.042 0.161 2322 Planarity : 0.005 0.095 2742 Dihedral : 4.295 19.773 2099 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.27 % Allowed : 30.02 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.19), residues: 1891 helix: 1.98 (0.33), residues: 277 sheet: -0.96 (0.29), residues: 347 loop : -1.93 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 54 TYR 0.017 0.001 TYR C 308 PHE 0.023 0.001 PHE H 67 TRP 0.025 0.001 TRP A 127 HIS 0.006 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00266 (15796) covalent geometry : angle 0.60756 (21428) SS BOND : bond 0.00297 ( 18) SS BOND : angle 0.69159 ( 36) hydrogen bonds : bond 0.04259 ( 405) hydrogen bonds : angle 5.06387 ( 1104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6304 (pt) REVERT: A 241 ASP cc_start: 0.7312 (p0) cc_final: 0.7108 (p0) REVERT: A 274 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6300 (tpp) REVERT: A 295 GLN cc_start: 0.6295 (pt0) cc_final: 0.6068 (pt0) REVERT: B 77 MET cc_start: 0.7988 (mmm) cc_final: 0.7306 (mtt) REVERT: C 101 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4560 (t80) REVERT: D 46 ASN cc_start: 0.7756 (t0) cc_final: 0.7440 (t0) REVERT: D 63 PHE cc_start: 0.6292 (m-80) cc_final: 0.6078 (m-80) REVERT: D 77 MET cc_start: 0.7615 (mmt) cc_final: 0.7060 (mmm) REVERT: E 104 ASP cc_start: 0.7692 (p0) cc_final: 0.7470 (p0) REVERT: E 119 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6612 (tt0) REVERT: E 250 ASN cc_start: 0.5226 (OUTLIER) cc_final: 0.4579 (m110) REVERT: F 77 MET cc_start: 0.8121 (mmm) cc_final: 0.7764 (mtt) REVERT: H 29 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7381 (t80) REVERT: H 35 SER cc_start: 0.8520 (t) cc_final: 0.8285 (m) REVERT: H 57 THR cc_start: 0.8772 (m) cc_final: 0.8543 (p) REVERT: J 29 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7325 (t80) REVERT: K 42 GLN cc_start: 0.8312 (pt0) cc_final: 0.8093 (pt0) REVERT: K 103 LYS cc_start: 0.7953 (ptmm) cc_final: 0.7278 (mmmt) REVERT: L 54 ARG cc_start: 0.7730 (tpt170) cc_final: 0.6683 (tpp-160) REVERT: M 35 SER cc_start: 0.8746 (t) cc_final: 0.8418 (m) REVERT: M 43 LYS cc_start: 0.7527 (ptmm) cc_final: 0.7285 (pttt) REVERT: N 21 LEU cc_start: 0.7885 (tt) cc_final: 0.7160 (mp) outliers start: 90 outliers final: 69 residues processed: 336 average time/residue: 0.1050 time to fit residues: 55.5667 Evaluate side-chains 343 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 267 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 53 optimal weight: 0.0770 chunk 107 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 175 optimal weight: 0.0170 chunk 180 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 184 HIS ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN H 39 GLN J 39 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.192890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.168437 restraints weight = 26775.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.170769 restraints weight = 20333.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.172162 restraints weight = 16624.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.173684 restraints weight = 14501.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.174616 restraints weight = 12968.444| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15814 Z= 0.108 Angle : 0.604 11.374 21464 Z= 0.307 Chirality : 0.041 0.157 2322 Planarity : 0.005 0.094 2742 Dihedral : 4.126 18.353 2099 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.92 % Allowed : 31.42 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.19), residues: 1891 helix: 2.03 (0.33), residues: 277 sheet: -0.97 (0.28), residues: 357 loop : -1.83 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 76 TYR 0.014 0.001 TYR C 308 PHE 0.019 0.001 PHE H 67 TRP 0.022 0.001 TRP A 127 HIS 0.005 0.001 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00240 (15796) covalent geometry : angle 0.60446 (21428) SS BOND : bond 0.00219 ( 18) SS BOND : angle 0.58659 ( 36) hydrogen bonds : bond 0.04030 ( 405) hydrogen bonds : angle 4.89456 ( 1104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TYR cc_start: 0.7107 (t80) cc_final: 0.6798 (t80) REVERT: A 237 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6463 (pt) REVERT: A 274 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6216 (tpp) REVERT: A 295 GLN cc_start: 0.6248 (pt0) cc_final: 0.6029 (pt0) REVERT: B 77 MET cc_start: 0.7875 (mmm) cc_final: 0.7325 (mtt) REVERT: C 101 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.4527 (t80) REVERT: D 46 ASN cc_start: 0.7549 (t0) cc_final: 0.7220 (t0) REVERT: D 77 MET cc_start: 0.7357 (mmt) cc_final: 0.6868 (mmm) REVERT: E 104 ASP cc_start: 0.7690 (p0) cc_final: 0.7459 (p0) REVERT: E 250 ASN cc_start: 0.4618 (OUTLIER) cc_final: 0.4002 (m110) REVERT: F 77 MET cc_start: 0.8064 (mmm) cc_final: 0.7701 (mtt) REVERT: H 29 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7295 (t80) REVERT: H 57 THR cc_start: 0.8789 (m) cc_final: 0.8576 (p) REVERT: J 29 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7217 (t80) REVERT: K 103 LYS cc_start: 0.7908 (ptmm) cc_final: 0.7212 (mmmt) REVERT: L 54 ARG cc_start: 0.7643 (tpt170) cc_final: 0.6543 (tpp-160) REVERT: N 21 LEU cc_start: 0.7792 (tt) cc_final: 0.7102 (mp) outliers start: 67 outliers final: 57 residues processed: 319 average time/residue: 0.1030 time to fit residues: 51.3472 Evaluate side-chains 327 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 270 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 107 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 28 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN D 47 GLN H 39 GLN J 39 GLN J 82AASN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.185070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.161978 restraints weight = 27103.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.162386 restraints weight = 22684.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163626 restraints weight = 23143.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.163940 restraints weight = 17778.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164268 restraints weight = 17778.935| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15814 Z= 0.197 Angle : 0.695 11.317 21464 Z= 0.356 Chirality : 0.044 0.177 2322 Planarity : 0.006 0.104 2742 Dihedral : 4.605 19.767 2099 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.45 % Allowed : 31.07 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.19), residues: 1891 helix: 1.81 (0.33), residues: 275 sheet: -0.99 (0.29), residues: 342 loop : -2.08 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 76 TYR 0.020 0.002 TYR A 105 PHE 0.031 0.002 PHE H 67 TRP 0.033 0.002 TRP E 153 HIS 0.008 0.002 HIS E 184 Details of bonding type rmsd covalent geometry : bond 0.00466 (15796) covalent geometry : angle 0.69393 (21428) SS BOND : bond 0.00448 ( 18) SS BOND : angle 1.01418 ( 36) hydrogen bonds : bond 0.04972 ( 405) hydrogen bonds : angle 5.23715 ( 1104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3782 Ramachandran restraints generated. 1891 Oldfield, 0 Emsley, 1891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 TYR cc_start: 0.7530 (OUTLIER) cc_final: 0.7028 (m-80) REVERT: A 237 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6514 (pt) REVERT: A 274 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.6113 (tpp) REVERT: B 77 MET cc_start: 0.8110 (mmm) cc_final: 0.7693 (mtt) REVERT: C 101 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.4628 (t80) REVERT: C 231 ASN cc_start: 0.5746 (OUTLIER) cc_final: 0.5321 (p0) REVERT: D 46 ASN cc_start: 0.7653 (t0) cc_final: 0.7340 (t0) REVERT: D 77 MET cc_start: 0.7809 (mmt) cc_final: 0.7147 (mtt) REVERT: E 48 ASN cc_start: 0.7677 (m-40) cc_final: 0.7370 (m-40) REVERT: E 104 ASP cc_start: 0.7705 (p0) cc_final: 0.7448 (p0) REVERT: E 119 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6872 (tt0) REVERT: F 24 TYR cc_start: 0.8448 (m-80) cc_final: 0.8113 (m-80) REVERT: F 77 MET cc_start: 0.8484 (mmm) cc_final: 0.7492 (mtt) REVERT: H 29 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7387 (t80) REVERT: J 29 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7462 (t80) REVERT: K 42 GLN cc_start: 0.8306 (pt0) cc_final: 0.8048 (pt0) REVERT: K 103 LYS cc_start: 0.8021 (ptmm) cc_final: 0.7253 (mmmt) REVERT: L 54 ARG cc_start: 0.7789 (tpt170) cc_final: 0.6695 (tpp-160) REVERT: N 21 LEU cc_start: 0.7818 (tt) cc_final: 0.7074 (mp) REVERT: N 94 TRP cc_start: 0.8121 (t-100) cc_final: 0.7616 (t-100) outliers start: 76 outliers final: 59 residues processed: 316 average time/residue: 0.1073 time to fit residues: 52.7840 Evaluate side-chains 321 residues out of total 1709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 TYR Chi-restraints excluded: chain A residue 127 TRP Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain B residue 9 PHE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 PHE Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 250 ASN Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 145 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN D 47 GLN H 39 GLN J 39 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.185699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.162070 restraints weight = 26900.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.163400 restraints weight = 23098.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.164704 restraints weight = 21936.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.165008 restraints weight = 17401.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165734 restraints weight = 17654.269| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15814 Z= 0.156 Angle : 0.665 11.404 21464 Z= 0.339 Chirality : 0.043 0.166 2322 Planarity : 0.005 0.099 2742 Dihedral : 4.582 19.299 2099 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.33 % Allowed : 31.83 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.19), residues: 1891 helix: 1.86 (0.33), residues: 275 sheet: -0.93 (0.30), residues: 334 loop : -2.08 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 76 TYR 0.016 0.001 TYR F 159 PHE 0.030 0.002 PHE H 67 TRP 0.029 0.002 TRP A 127 HIS 0.007 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00367 (15796) covalent geometry : angle 0.66442 (21428) SS BOND : bond 0.00387 ( 18) SS BOND : angle 0.84672 ( 36) hydrogen bonds : bond 0.04747 ( 405) hydrogen bonds : angle 5.14672 ( 1104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.83 seconds wall clock time: 44 minutes 47.97 seconds (2687.97 seconds total)