Starting phenix.real_space_refine on Fri Jul 3 08:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.cif" model { file = "/net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do6_27593/07_2026/8do6_27593.map" } resolution = 3.1 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= 0.039 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: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 24 5.16 5 C 8030 2.51 5 N 2198 2.21 5 O 2667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12980 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 15, 'rna3p': 19} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 13} Link IDs: {'rna2p': 3, 'rna3p': 22} Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 926 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 951 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "H" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2671 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.24 Number of scatterers: 12980 At special positions: 0 Unit cell: (93.906, 95.598, 164.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 61 15.00 O 2667 8.00 N 2198 7.00 C 8030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.13 Conformation dependent library (CDL) restraints added in 605.2 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 20 sheets defined 40.8% alpha, 21.7% beta 17 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'E' and resid 47 through 65 Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.788A pdb=" N LEU E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 removed outlier: 3.530A pdb=" N ASN E 114 " --> pdb=" O HIS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 161 through 178 removed outlier: 4.953A pdb=" N GLU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 64 Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.796A pdb=" N LEU G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 113 Processing helix chain 'G' and resid 158 through 160 No H-bonds generated for 'chain 'G' and resid 158 through 160' Processing helix chain 'G' and resid 161 through 178 removed outlier: 4.080A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 188 Processing helix chain 'F' and resid 47 through 64 Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 104 through 114 removed outlier: 3.702A pdb=" N GLU F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 179 Processing helix chain 'F' and resid 184 through 188 removed outlier: 3.517A pdb=" N GLY F 188 " --> pdb=" O GLY F 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 24 removed outlier: 3.625A pdb=" N ASN C 24 " --> pdb=" O VAL C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 removed outlier: 4.246A pdb=" N GLN C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 4.067A pdb=" N GLU C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.664A pdb=" N ASP C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.649A pdb=" N ILE C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 136 Processing helix chain 'D' and resid 16 through 24 removed outlier: 3.653A pdb=" N VAL D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 65 removed outlier: 4.539A pdb=" N GLN D 54 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.581A pdb=" N ILE D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 136 removed outlier: 3.793A pdb=" N VAL D 131 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.708A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.727A pdb=" N THR B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 186 removed outlier: 4.480A pdb=" N TYR B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.870A pdb=" N LEU B 236 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 53 removed outlier: 3.665A pdb=" N LYS H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.698A pdb=" N ASN H 61 " --> pdb=" O TYR H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 83 removed outlier: 4.017A pdb=" N TYR H 78 " --> pdb=" O GLY H 74 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 91 removed outlier: 3.777A pdb=" N GLU H 88 " --> pdb=" O LYS H 85 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLU H 90 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA H 91 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 147 Processing helix chain 'H' and resid 167 through 169 No H-bonds generated for 'chain 'H' and resid 167 through 169' Processing helix chain 'H' and resid 211 through 230 Processing helix chain 'H' and resid 231 through 236 removed outlier: 4.013A pdb=" N GLU H 236 " --> pdb=" O GLY H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 246 Processing helix chain 'H' and resid 266 through 270 Processing helix chain 'H' and resid 271 through 276 removed outlier: 3.877A pdb=" N LYS H 276 " --> pdb=" O HIS H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 293 Processing helix chain 'H' and resid 296 through 300 Processing sheet with id=AA1, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.748A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL E 203 " --> pdb=" O LYS E 4 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS E 6 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR E 201 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER E 8 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 199 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR E 10 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N THR E 197 " --> pdb=" O THR E 10 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU E 12 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS E 195 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.748A pdb=" N PHE E 102 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER E 3 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLY B 194 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE E 98 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 119 through 125 Processing sheet with id=AA4, first strand: chain 'G' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'G' and resid 45 through 46 removed outlier: 4.198A pdb=" N SER G 3 " --> pdb=" O VAL G 156 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS G 4 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR G 10 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP G 196 " --> pdb=" O THR G 10 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU G 12 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE G 194 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 122 through 123 Processing sheet with id=AA7, first strand: chain 'F' and resid 96 through 97 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.543A pdb=" N LYS F 4 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR F 201 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS F 6 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE F 199 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER F 8 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR F 197 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 119 through 120 Processing sheet with id=AB1, first strand: chain 'F' and resid 123 through 124 Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 26 removed outlier: 3.520A pdb=" N LYS D 26 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 59 removed outlier: 7.346A pdb=" N ALA B 159 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 12 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'B' and resid 124 through 133 Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 246 Processing sheet with id=AB8, first strand: chain 'B' and resid 281 through 284 Processing sheet with id=AB9, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.741A pdb=" N TYR H 6 " --> pdb=" O LEU H 203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE H 205 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS H 4 " --> pdb=" O ILE H 205 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN H 5 " --> pdb=" O LEU H 335 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 19 through 24 removed outlier: 4.857A pdb=" N GLN H 22 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET H 119 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ILE H 193 " --> pdb=" O MET H 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 186 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP H 178 " --> pdb=" O MET H 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU H 188 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 13.748A pdb=" N LEU H 171 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N SER H 96 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ILE H 173 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS H 98 " --> pdb=" O ILE H 173 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLN H 175 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASN H 100 " --> pdb=" O GLN H 175 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE H 177 " --> pdb=" O ASN H 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 19 through 24 removed outlier: 4.857A pdb=" N GLN H 22 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET H 119 " --> pdb=" O GLU H 191 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ILE H 193 " --> pdb=" O MET H 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET H 186 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP H 178 " --> pdb=" O MET H 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU H 188 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN H 175 " --> pdb=" O THR H 315 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR H 315 " --> pdb=" O GLN H 175 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 1 1.21 - 1.36: 4132 1.36 - 1.51: 4418 1.51 - 1.66: 4745 1.66 - 1.81: 44 Bond restraints: 13340 Sorted by residual: bond pdb=" CG PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 1.503 1.065 0.438 3.40e-02 8.65e+02 1.66e+02 bond pdb=" N PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" CB PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CB ASN H 147 " pdb=" CG ASN H 147 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.39e+00 bond pdb=" CB GLU B 158 " pdb=" CG GLU B 158 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 13335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 18200 4.90 - 9.80: 30 9.80 - 14.71: 2 14.71 - 19.61: 1 19.61 - 24.51: 1 Bond angle restraints: 18234 Sorted by residual: angle pdb=" N PRO H 70 " pdb=" CD PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 103.20 78.69 24.51 1.50e+00 4.44e-01 2.67e+02 angle pdb=" CA PRO H 70 " pdb=" CB PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 104.50 89.09 15.41 1.90e+00 2.77e-01 6.58e+01 angle pdb=" CA PRO H 70 " pdb=" N PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 112.00 102.87 9.13 1.40e+00 5.10e-01 4.25e+01 angle pdb=" N PRO H 70 " pdb=" CA PRO H 70 " pdb=" CB PRO H 70 " ideal model delta sigma weight residual 102.60 97.16 5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" O4' A I 27 " pdb=" C1' A I 27 " pdb=" N9 A I 27 " ideal model delta sigma weight residual 108.20 114.47 -6.27 1.50e+00 4.44e-01 1.75e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 7631 34.52 - 69.04: 239 69.04 - 103.57: 27 103.57 - 138.09: 1 138.09 - 172.61: 1 Dihedral angle restraints: 7899 sinusoidal: 3701 harmonic: 4198 Sorted by residual: dihedral pdb=" O4' U I 26 " pdb=" C1' U I 26 " pdb=" N1 U I 26 " pdb=" C2 U I 26 " ideal model delta sinusoidal sigma weight residual -128.00 44.61 -172.61 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " pdb=" C2 C I 8 " ideal model delta sinusoidal sigma weight residual -128.00 7.31 -135.31 1 1.70e+01 3.46e-03 5.68e+01 dihedral pdb=" CA SER F 160 " pdb=" C SER F 160 " pdb=" N GLN F 161 " pdb=" CA GLN F 161 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1738 0.055 - 0.111: 266 0.111 - 0.166: 41 0.166 - 0.222: 4 0.222 - 0.277: 3 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C1' A I 27 " pdb=" O4' A I 27 " pdb=" C2' A I 27 " pdb=" N9 A I 27 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1' G I 21 " pdb=" O4' G I 21 " pdb=" C2' G I 21 " pdb=" N9 G I 21 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU B 211 " pdb=" CB LEU B 211 " pdb=" CD1 LEU B 211 " pdb=" CD2 LEU B 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2049 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.058 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 157 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " -0.036 2.00e-02 2.50e+03 1.79e-02 8.82e+00 pdb=" N9 A I 27 " 0.046 2.00e-02 2.50e+03 pdb=" C8 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A I 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A I 27 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A I 27 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " -0.037 2.00e-02 2.50e+03 1.70e-02 8.70e+00 pdb=" N9 G I 21 " 0.044 2.00e-02 2.50e+03 pdb=" C8 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G I 21 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G I 21 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G I 21 " 0.004 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 521 2.70 - 3.25: 13278 3.25 - 3.80: 22147 3.80 - 4.35: 29926 4.35 - 4.90: 47743 Nonbonded interactions: 113615 Sorted by model distance: nonbonded pdb=" OP1 U J 15 " pdb=" OG1 THR D 44 " model vdw 2.146 3.040 nonbonded pdb=" OP1 A I 27 " pdb=" OG SER H 132 " model vdw 2.173 3.040 nonbonded pdb=" O PHE D 98 " pdb=" OG1 THR D 102 " model vdw 2.174 3.040 nonbonded pdb=" OP2 A I 1 " pdb=" OG SER B 37 " model vdw 2.181 3.040 nonbonded pdb=" OP1 C I 31 " pdb=" OH TYR H 297 " model vdw 2.184 3.040 ... (remaining 113610 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 'C' and (resid 16 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 136)) selection = (chain 'D' and (resid 16 through 24 or resid 37 through 136)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.420 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.005 0.438 13340 Z= 0.190 Angle : 0.679 24.509 18234 Z= 0.368 Chirality : 0.043 0.277 2052 Planarity : 0.005 0.085 2120 Dihedral : 16.563 172.610 5207 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.33 % Favored : 93.25 % Rotamer: Outliers : 0.62 % Allowed : 13.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1422 helix: 0.38 (0.23), residues: 526 sheet: -1.20 (0.30), residues: 297 loop : -1.60 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 64 TYR 0.022 0.002 TYR C 87 PHE 0.019 0.002 PHE D 74 TRP 0.005 0.001 TRP H 230 HIS 0.005 0.001 HIS H 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.19 (13340) covalent geometry : angle 0.67940 / 0.37 (18234) hydrogen bonds : bond 0.16554 / 11.31 ( 548) hydrogen bonds : angle 7.19373 / 5.01 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.494 Fit side-chains REVERT: D 110 ARG cc_start: 0.6254 (mtm180) cc_final: 0.6001 (mtp180) REVERT: B 226 MET cc_start: 0.5894 (tpp) cc_final: 0.5360 (mpp) REVERT: B 283 PHE cc_start: 0.7613 (m-80) cc_final: 0.7367 (m-80) REVERT: H 85 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7656 (pttp) REVERT: H 186 MET cc_start: 0.7880 (tpp) cc_final: 0.7095 (tpp) outliers start: 8 outliers final: 3 residues processed: 222 average time/residue: 0.1199 time to fit residues: 39.0272 Evaluate side-chains 206 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain B residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 GLN E 110 HIS G 57 ASN F 125 ASN C 24 ASN D 24 ASN B 183 GLN B 206 GLN H 54 ASN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 148 ASN H 255 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146890 restraints weight = 21379.578| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.30 r_work: 0.3793 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13340 Z= 0.131 Angle : 0.582 9.589 18234 Z= 0.314 Chirality : 0.042 0.371 2052 Planarity : 0.004 0.049 2120 Dihedral : 11.307 175.685 2296 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.47 % Favored : 93.18 % Rotamer: Outliers : 1.95 % Allowed : 13.48 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.22), residues: 1422 helix: 0.88 (0.23), residues: 537 sheet: -1.00 (0.30), residues: 290 loop : -1.61 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 137 TYR 0.026 0.001 TYR H 226 PHE 0.017 0.001 PHE G 166 TRP 0.004 0.001 TRP B 52 HIS 0.004 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (13340) covalent geometry : angle 0.58212 / 0.31 (18234) hydrogen bonds : bond 0.04563 / 3.25 ( 548) hydrogen bonds : angle 5.48751 / 3.83 ( 1572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7248 (mm-30) REVERT: C 118 LYS cc_start: 0.7993 (mppt) cc_final: 0.7120 (ttpp) REVERT: D 26 LYS cc_start: 0.6225 (pptt) cc_final: 0.6006 (pptt) REVERT: B 158 GLU cc_start: 0.7772 (mp0) cc_final: 0.7571 (mp0) REVERT: B 226 MET cc_start: 0.5917 (tpp) cc_final: 0.5208 (mpp) REVERT: H 186 MET cc_start: 0.7832 (tpp) cc_final: 0.7558 (mmt) outliers start: 25 outliers final: 12 residues processed: 269 average time/residue: 0.1220 time to fit residues: 47.5155 Evaluate side-chains 220 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS E 125 ASN G 18 HIS G 97 GLN C 71 ASN B 206 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.158356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136503 restraints weight = 21620.446| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.32 r_work: 0.3654 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13340 Z= 0.285 Angle : 0.703 9.806 18234 Z= 0.375 Chirality : 0.048 0.418 2052 Planarity : 0.005 0.054 2120 Dihedral : 11.678 172.931 2290 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.16 % Favored : 91.49 % Rotamer: Outliers : 3.35 % Allowed : 14.58 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.21), residues: 1422 helix: 0.65 (0.22), residues: 526 sheet: -1.20 (0.30), residues: 287 loop : -1.78 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 137 TYR 0.023 0.002 TYR H 226 PHE 0.032 0.002 PHE D 120 TRP 0.013 0.002 TRP H 230 HIS 0.008 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 (13340) covalent geometry : angle 0.70255 / 0.38 (18234) hydrogen bonds : bond 0.05159 / 3.56 ( 548) hydrogen bonds : angle 5.73980 / 4.01 ( 1572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 215 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: G 140 GLU cc_start: 0.7980 (pm20) cc_final: 0.7755 (pm20) REVERT: F 159 GLU cc_start: 0.5727 (tm-30) cc_final: 0.5341 (tm-30) REVERT: F 171 LYS cc_start: 0.7591 (mtpt) cc_final: 0.7380 (mtpt) REVERT: F 180 TYR cc_start: 0.8067 (p90) cc_final: 0.7783 (p90) REVERT: C 109 ASP cc_start: 0.8823 (t0) cc_final: 0.8573 (t0) REVERT: C 118 LYS cc_start: 0.8064 (mppt) cc_final: 0.7178 (ttpp) REVERT: D 77 GLU cc_start: 0.6820 (tp30) cc_final: 0.6410 (tp30) REVERT: D 130 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7340 (mm) REVERT: B 158 GLU cc_start: 0.7894 (mp0) cc_final: 0.7481 (mp0) REVERT: H 198 GLU cc_start: 0.6893 (mp0) cc_final: 0.6385 (pm20) REVERT: H 283 GLN cc_start: 0.5692 (OUTLIER) cc_final: 0.5345 (pm20) outliers start: 43 outliers final: 22 residues processed: 244 average time/residue: 0.1199 time to fit residues: 42.6439 Evaluate side-chains 227 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 202 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 52 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS G 97 GLN C 71 ASN D 56 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139427 restraints weight = 21564.888| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.37 r_work: 0.3686 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13340 Z= 0.183 Angle : 0.612 8.383 18234 Z= 0.330 Chirality : 0.045 0.405 2052 Planarity : 0.004 0.048 2120 Dihedral : 11.548 175.101 2290 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 2.81 % Allowed : 17.77 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.22), residues: 1422 helix: 0.77 (0.22), residues: 533 sheet: -1.14 (0.31), residues: 278 loop : -1.70 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 64 TYR 0.013 0.001 TYR F 180 PHE 0.027 0.002 PHE D 120 TRP 0.003 0.001 TRP H 230 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (13340) covalent geometry : angle 0.61178 / 0.33 (18234) hydrogen bonds : bond 0.04542 / 3.19 ( 548) hydrogen bonds : angle 5.48219 / 3.83 ( 1572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: G 140 GLU cc_start: 0.7933 (pm20) cc_final: 0.7667 (pm20) REVERT: F 159 GLU cc_start: 0.5633 (tm-30) cc_final: 0.5265 (tm-30) REVERT: F 171 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7246 (mtpt) REVERT: C 73 GLU cc_start: 0.7763 (mt-10) cc_final: 0.6533 (tp30) REVERT: C 118 LYS cc_start: 0.8023 (mppt) cc_final: 0.7120 (ttpp) REVERT: D 77 GLU cc_start: 0.6795 (tp30) cc_final: 0.6355 (tp30) REVERT: D 130 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7362 (mm) REVERT: B 28 MET cc_start: 0.6757 (pmm) cc_final: 0.6546 (pmm) REVERT: B 158 GLU cc_start: 0.7931 (mp0) cc_final: 0.7518 (mp0) REVERT: H 198 GLU cc_start: 0.7008 (mp0) cc_final: 0.6394 (pm20) REVERT: H 283 GLN cc_start: 0.5683 (OUTLIER) cc_final: 0.5375 (pm20) outliers start: 36 outliers final: 25 residues processed: 236 average time/residue: 0.1181 time to fit residues: 41.1150 Evaluate side-chains 227 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS G 97 GLN C 71 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 206 GLN H 60 GLN H 114 ASN H 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.161992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140132 restraints weight = 21722.046| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.38 r_work: 0.3697 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13340 Z= 0.172 Angle : 0.609 8.197 18234 Z= 0.327 Chirality : 0.044 0.398 2052 Planarity : 0.004 0.046 2120 Dihedral : 11.497 175.035 2290 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.03 % Favored : 92.62 % Rotamer: Outliers : 3.59 % Allowed : 17.69 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1422 helix: 0.83 (0.23), residues: 533 sheet: -1.23 (0.31), residues: 277 loop : -1.68 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 64 TYR 0.016 0.001 TYR C 87 PHE 0.024 0.002 PHE D 120 TRP 0.004 0.001 TRP H 230 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (13340) covalent geometry : angle 0.60871 / 0.33 (18234) hydrogen bonds : bond 0.04464 / 3.16 ( 548) hydrogen bonds : angle 5.40127 / 3.78 ( 1572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: G 140 GLU cc_start: 0.7908 (pm20) cc_final: 0.7616 (pm20) REVERT: F 81 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7682 (ptp-170) REVERT: F 171 LYS cc_start: 0.7487 (mtpt) cc_final: 0.7248 (mtpt) REVERT: C 63 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 118 LYS cc_start: 0.8025 (mppt) cc_final: 0.7132 (ttpp) REVERT: D 63 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: D 77 GLU cc_start: 0.6795 (tp30) cc_final: 0.6352 (tp30) REVERT: D 130 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7413 (mm) REVERT: B 158 GLU cc_start: 0.7921 (mp0) cc_final: 0.7488 (mp0) REVERT: H 198 GLU cc_start: 0.7036 (mp0) cc_final: 0.6420 (pm20) REVERT: H 224 LYS cc_start: 0.7705 (tttt) cc_final: 0.6836 (tmtt) REVERT: H 283 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5427 (pm20) outliers start: 46 outliers final: 29 residues processed: 236 average time/residue: 0.1170 time to fit residues: 40.2367 Evaluate side-chains 236 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 105 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 98 optimal weight: 0.0770 chunk 106 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS G 97 GLN C 41 ASN C 71 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 207 GLN H 148 ASN H 272 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144011 restraints weight = 21406.682| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.38 r_work: 0.3743 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13340 Z= 0.128 Angle : 0.579 10.253 18234 Z= 0.310 Chirality : 0.043 0.371 2052 Planarity : 0.004 0.043 2120 Dihedral : 11.406 175.737 2290 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.19 % Favored : 93.46 % Rotamer: Outliers : 3.35 % Allowed : 18.71 % Favored : 77.94 % 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 are not related in a simple way. whole: -0.92 (0.22), residues: 1422 helix: 0.85 (0.23), residues: 541 sheet: -1.18 (0.30), residues: 288 loop : -1.65 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 64 TYR 0.016 0.001 TYR H 223 PHE 0.021 0.001 PHE D 120 TRP 0.003 0.001 TRP H 230 HIS 0.004 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13340) covalent geometry : angle 0.57918 / 0.31 (18234) hydrogen bonds : bond 0.04182 / 2.98 ( 548) hydrogen bonds : angle 5.19146 / 3.65 ( 1572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7369 (mm-30) REVERT: G 138 GLN cc_start: 0.7886 (tt0) cc_final: 0.7445 (mt0) REVERT: F 92 GLN cc_start: 0.6950 (pm20) cc_final: 0.6616 (pm20) REVERT: F 147 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: F 171 LYS cc_start: 0.7485 (mtpt) cc_final: 0.7240 (mtpt) REVERT: F 180 TYR cc_start: 0.7971 (p90) cc_final: 0.7743 (p90) REVERT: C 22 LYS cc_start: 0.5007 (mmtt) cc_final: 0.4723 (mmtt) REVERT: C 63 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7118 (t80) REVERT: C 118 LYS cc_start: 0.8002 (mppt) cc_final: 0.7106 (ttpp) REVERT: D 63 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: D 77 GLU cc_start: 0.6792 (tp30) cc_final: 0.6361 (tp30) REVERT: D 84 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.5725 (tptt) REVERT: D 130 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7366 (mm) REVERT: B 28 MET cc_start: 0.6655 (pmm) cc_final: 0.6446 (pmm) REVERT: B 158 GLU cc_start: 0.7924 (mp0) cc_final: 0.7682 (mp0) REVERT: H 198 GLU cc_start: 0.6963 (mp0) cc_final: 0.6357 (pm20) REVERT: H 224 LYS cc_start: 0.7670 (tttt) cc_final: 0.6790 (tmtt) REVERT: H 272 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.6007 (m90) REVERT: H 283 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5275 (pm20) outliers start: 43 outliers final: 23 residues processed: 257 average time/residue: 0.1162 time to fit residues: 44.0311 Evaluate side-chains 230 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 272 HIS Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 44 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS G 97 GLN F 97 GLN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.162618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140604 restraints weight = 21666.074| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.37 r_work: 0.3705 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13340 Z= 0.174 Angle : 0.610 8.081 18234 Z= 0.329 Chirality : 0.044 0.389 2052 Planarity : 0.005 0.100 2120 Dihedral : 11.427 174.406 2290 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.89 % Favored : 92.76 % Rotamer: Outliers : 3.51 % Allowed : 19.56 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1422 helix: 0.84 (0.23), residues: 535 sheet: -1.17 (0.31), residues: 282 loop : -1.64 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 64 TYR 0.014 0.001 TYR H 223 PHE 0.028 0.002 PHE D 120 TRP 0.006 0.001 TRP H 230 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (13340) covalent geometry : angle 0.61047 / 0.33 (18234) hydrogen bonds : bond 0.04352 / 3.07 ( 548) hydrogen bonds : angle 5.23388 / 3.67 ( 1572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: G 138 GLN cc_start: 0.7886 (tt0) cc_final: 0.7488 (mt0) REVERT: F 147 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: F 171 LYS cc_start: 0.7520 (mtpt) cc_final: 0.7280 (mtpt) REVERT: F 180 TYR cc_start: 0.8126 (p90) cc_final: 0.7727 (p90) REVERT: C 22 LYS cc_start: 0.5123 (mmtt) cc_final: 0.4836 (mmtt) REVERT: C 63 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.7061 (t80) REVERT: C 88 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 118 LYS cc_start: 0.8027 (mppt) cc_final: 0.7122 (ttpp) REVERT: D 63 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: D 77 GLU cc_start: 0.6868 (tp30) cc_final: 0.6472 (tp30) REVERT: D 130 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7343 (mm) REVERT: B 129 GLN cc_start: 0.7694 (mt0) cc_final: 0.7456 (mt0) REVERT: B 158 GLU cc_start: 0.7915 (mp0) cc_final: 0.7667 (mp0) REVERT: B 226 MET cc_start: 0.6138 (tpp) cc_final: 0.5866 (tpp) REVERT: H 198 GLU cc_start: 0.7017 (mp0) cc_final: 0.6371 (pm20) REVERT: H 224 LYS cc_start: 0.7667 (tttt) cc_final: 0.6776 (tmtt) REVERT: H 283 GLN cc_start: 0.5631 (OUTLIER) cc_final: 0.5300 (pm20) outliers start: 45 outliers final: 30 residues processed: 236 average time/residue: 0.1102 time to fit residues: 37.8748 Evaluate side-chains 235 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS G 97 GLN F 97 GLN F 155 ASN B 106 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.162946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141142 restraints weight = 21484.805| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.35 r_work: 0.3709 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13340 Z= 0.162 Angle : 0.613 8.022 18234 Z= 0.330 Chirality : 0.044 0.389 2052 Planarity : 0.004 0.046 2120 Dihedral : 11.425 174.998 2290 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.75 % Favored : 92.90 % Rotamer: Outliers : 3.43 % Allowed : 20.27 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1422 helix: 0.81 (0.23), residues: 535 sheet: -1.18 (0.31), residues: 282 loop : -1.63 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.018 0.001 TYR B 65 PHE 0.023 0.002 PHE D 120 TRP 0.004 0.001 TRP H 230 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (13340) covalent geometry : angle 0.61312 / 0.33 (18234) hydrogen bonds : bond 0.04339 / 3.07 ( 548) hydrogen bonds : angle 5.24142 / 3.68 ( 1572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7348 (mm-30) REVERT: G 6 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7558 (ptpp) REVERT: F 42 LYS cc_start: 0.8803 (ttpt) cc_final: 0.8421 (ttpt) REVERT: F 147 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: F 171 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7278 (mtpt) REVERT: F 180 TYR cc_start: 0.8153 (p90) cc_final: 0.7744 (p90) REVERT: C 22 LYS cc_start: 0.5087 (mmtt) cc_final: 0.4825 (mmtt) REVERT: C 63 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (t80) REVERT: C 88 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: C 118 LYS cc_start: 0.7993 (mppt) cc_final: 0.7117 (ttpp) REVERT: D 63 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: D 77 GLU cc_start: 0.6825 (tp30) cc_final: 0.6431 (tp30) REVERT: D 84 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6749 (mmtt) REVERT: D 130 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7369 (mm) REVERT: B 129 GLN cc_start: 0.7643 (mt0) cc_final: 0.7342 (mt0) REVERT: B 158 GLU cc_start: 0.7897 (mp0) cc_final: 0.7621 (mp0) REVERT: H 198 GLU cc_start: 0.7015 (mp0) cc_final: 0.6368 (pm20) REVERT: H 224 LYS cc_start: 0.7654 (tttt) cc_final: 0.6763 (tmtt) REVERT: H 283 GLN cc_start: 0.5594 (OUTLIER) cc_final: 0.5259 (pm20) outliers start: 44 outliers final: 30 residues processed: 236 average time/residue: 0.1177 time to fit residues: 40.4111 Evaluate side-chains 235 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS E 135 ASN G 97 GLN F 97 GLN F 155 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.157672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.135490 restraints weight = 21726.724| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.38 r_work: 0.3633 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13340 Z= 0.281 Angle : 0.727 9.687 18234 Z= 0.386 Chirality : 0.049 0.430 2052 Planarity : 0.005 0.065 2120 Dihedral : 11.686 173.154 2290 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.72 % Favored : 90.93 % Rotamer: Outliers : 3.35 % Allowed : 20.42 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1422 helix: 0.60 (0.22), residues: 530 sheet: -1.45 (0.30), residues: 278 loop : -1.74 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 52 TYR 0.018 0.002 TYR C 87 PHE 0.025 0.002 PHE D 120 TRP 0.013 0.002 TRP H 230 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.28 (13340) covalent geometry : angle 0.72723 / 0.39 (18234) hydrogen bonds : bond 0.04954 / 3.45 ( 548) hydrogen bonds : angle 5.60911 / 3.92 ( 1572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: G 6 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7557 (ptpp) REVERT: F 147 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: F 171 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7311 (mtpt) REVERT: F 180 TYR cc_start: 0.8389 (p90) cc_final: 0.8170 (p90) REVERT: C 109 ASP cc_start: 0.8833 (t0) cc_final: 0.8618 (t0) REVERT: C 118 LYS cc_start: 0.8040 (mppt) cc_final: 0.7162 (ttpp) REVERT: D 63 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: D 77 GLU cc_start: 0.6887 (tp30) cc_final: 0.6495 (tp30) REVERT: D 84 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6708 (mmtt) REVERT: D 130 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7287 (mm) REVERT: B 129 GLN cc_start: 0.7716 (mt0) cc_final: 0.7453 (mt0) REVERT: B 158 GLU cc_start: 0.8059 (mp0) cc_final: 0.7601 (mp0) REVERT: B 226 MET cc_start: 0.6320 (tpp) cc_final: 0.5887 (mpp) REVERT: H 198 GLU cc_start: 0.7179 (mp0) cc_final: 0.6473 (pm20) REVERT: H 224 LYS cc_start: 0.7749 (tttt) cc_final: 0.6819 (tmtt) REVERT: H 283 GLN cc_start: 0.5406 (OUTLIER) cc_final: 0.5048 (mp10) REVERT: H 290 THR cc_start: 0.7052 (m) cc_final: 0.6743 (p) outliers start: 43 outliers final: 29 residues processed: 229 average time/residue: 0.1100 time to fit residues: 36.8005 Evaluate side-chains 221 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS E 135 ASN G 97 GLN F 97 GLN F 155 ASN D 56 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.162724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140809 restraints weight = 21649.025| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.37 r_work: 0.3705 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13340 Z= 0.158 Angle : 0.651 11.729 18234 Z= 0.347 Chirality : 0.046 0.403 2052 Planarity : 0.004 0.048 2120 Dihedral : 11.465 175.992 2290 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.11 % Rotamer: Outliers : 2.73 % Allowed : 21.04 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1422 helix: 0.72 (0.23), residues: 535 sheet: -1.27 (0.31), residues: 276 loop : -1.69 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 64 TYR 0.027 0.002 TYR C 87 PHE 0.027 0.002 PHE C 63 TRP 0.003 0.001 TRP H 230 HIS 0.003 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (13340) covalent geometry : angle 0.65133 / 0.35 (18234) hydrogen bonds : bond 0.04408 / 3.14 ( 548) hydrogen bonds : angle 5.36385 / 3.75 ( 1572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: G 6 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7556 (ptpp) REVERT: G 138 GLN cc_start: 0.7929 (tt0) cc_final: 0.7528 (mt0) REVERT: F 28 ILE cc_start: 0.6568 (mt) cc_final: 0.6340 (mt) REVERT: F 92 GLN cc_start: 0.7013 (pm20) cc_final: 0.6689 (pm20) REVERT: F 147 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: F 171 LYS cc_start: 0.7566 (mtpt) cc_final: 0.7308 (mtpt) REVERT: C 22 LYS cc_start: 0.5060 (mmtt) cc_final: 0.4799 (mmtt) REVERT: C 118 LYS cc_start: 0.8013 (mppt) cc_final: 0.7130 (ttpp) REVERT: D 63 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: D 77 GLU cc_start: 0.6867 (tp30) cc_final: 0.6458 (tp30) REVERT: D 84 LYS cc_start: 0.7049 (mmtt) cc_final: 0.6752 (mmtt) REVERT: D 97 GLU cc_start: 0.7271 (mp0) cc_final: 0.7065 (mp0) REVERT: D 130 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7381 (mm) REVERT: B 129 GLN cc_start: 0.7646 (mt0) cc_final: 0.7357 (mt0) REVERT: B 158 GLU cc_start: 0.8004 (mp0) cc_final: 0.7555 (mp0) REVERT: B 226 MET cc_start: 0.6263 (tpp) cc_final: 0.5878 (tpp) REVERT: H 198 GLU cc_start: 0.7091 (mp0) cc_final: 0.6453 (pm20) REVERT: H 224 LYS cc_start: 0.7668 (tttt) cc_final: 0.6773 (tmtt) REVERT: H 283 GLN cc_start: 0.5418 (OUTLIER) cc_final: 0.5075 (mp10) outliers start: 35 outliers final: 24 residues processed: 226 average time/residue: 0.1036 time to fit residues: 33.9710 Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 283 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS E 135 ASN G 97 GLN F 97 GLN F 155 ASN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132704 restraints weight = 21799.722| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.38 r_work: 0.3593 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 13340 Z= 0.362 Angle : 0.820 12.468 18234 Z= 0.433 Chirality : 0.053 0.457 2052 Planarity : 0.005 0.068 2120 Dihedral : 11.875 173.305 2290 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.28 % Favored : 90.37 % Rotamer: Outliers : 3.43 % Allowed : 21.12 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1422 helix: 0.38 (0.22), residues: 527 sheet: -1.59 (0.31), residues: 268 loop : -1.85 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.031 0.003 TYR C 87 PHE 0.035 0.003 PHE C 63 TRP 0.018 0.003 TRP H 230 HIS 0.009 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.36 (13340) covalent geometry : angle 0.82013 / 0.43 (18234) hydrogen bonds : bond 0.05435 / 3.75 ( 548) hydrogen bonds : angle 5.85998 / 4.10 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2951.38 seconds wall clock time: 51 minutes 50.34 seconds (3110.34 seconds total)