Starting phenix.real_space_refine on Sat Aug 23 15:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do6_27593/08_2025/8do6_27593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do6_27593/08_2025/8do6_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 { model { file = "/net/cci-nas-00/data/ceres_data/8do6_27593/08_2025/8do6_27593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do6_27593/08_2025/8do6_27593.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8do6_27593/08_2025/8do6_27593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do6_27593/08_2025/8do6_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.01, per 1000 atoms: 0.23 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: 0.97 Conformation dependent library (CDL) restraints added in 537.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.47 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: 1.98 Time building geometry restraints manager: 1.30 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: 7718 34.52 - 69.04: 319 69.04 - 103.57: 38 103.57 - 138.09: 1 138.09 - 172.61: 1 Dihedral angle restraints: 8077 sinusoidal: 3879 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 8074 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.560 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 18.001 172.610 5385 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 aren 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 covalent geometry : bond 0.00507 (13340) covalent geometry : angle 0.67940 (18234) hydrogen bonds : bond 0.16554 ( 548) hydrogen bonds : angle 7.19373 ( 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 : 0.438 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: 0.7612 (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: 0.1088 time to fit residues: 35.1115 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 : 0.531 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 57 ASN F 125 ASN F 135 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146836 restraints weight = 21356.478| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.29 r_work: 0.3790 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1188 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= 0.132 Angle : 0.583 9.499 18234 Z= 0.315 Chirality : 0.042 0.369 2052 Planarity : 0.004 0.049 2120 Dihedral : 15.477 175.477 2474 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Rotamer: Outliers : 1.95 % Allowed : 13.64 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.22), residues: 1422 helix: 0.88 (0.23), residues: 537 sheet: -1.01 (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 D 74 TRP 0.005 0.001 TRP B 52 HIS 0.004 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00278 (13340) covalent geometry : angle 0.58254 (18234) hydrogen bonds : bond 0.04591 ( 548) hydrogen bonds : angle 5.49692 ( 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 279 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: C 118 LYS cc_start: 0.7986 (mppt) cc_final: 0.7114 (ttpp) REVERT: D 26 LYS cc_start: 0.6257 (pptt) cc_final: 0.6039 (pptt) REVERT: B 226 MET cc_start: 0.5929 (tpp) cc_final: 0.5214 (mpp) REVERT: H 186 MET cc_start: 0.7860 (tpp) cc_final: 0.7581 (mmt) outliers start: 25 outliers final: 12 residues processed: 268 average time/residue: 0.1110 time to fit residues: 42.7732 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 : 0.460 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS E 125 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.161980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140514 restraints weight = 21456.147| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.30 r_work: 0.3708 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13340 Z= 0.201 Angle : 0.621 8.881 18234 Z= 0.334 Chirality : 0.045 0.387 2052 Planarity : 0.004 0.050 2120 Dihedral : 15.426 173.343 2468 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.31 % Favored : 92.33 % Rotamer: Outliers : 2.73 % Allowed : 14.81 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.22), residues: 1422 helix: 0.80 (0.23), residues: 535 sheet: -1.02 (0.31), residues: 284 loop : -1.64 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 137 TYR 0.024 0.002 TYR H 226 PHE 0.033 0.002 PHE D 120 TRP 0.009 0.001 TRP H 230 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00448 (13340) covalent geometry : angle 0.62110 (18234) hydrogen bonds : bond 0.04675 ( 548) hydrogen bonds : angle 5.50404 ( 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 257 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: F 159 GLU cc_start: 0.5706 (tm-30) cc_final: 0.5459 (tm-30) REVERT: F 171 LYS cc_start: 0.7488 (mtpt) cc_final: 0.7276 (mtpt) REVERT: C 118 LYS cc_start: 0.8024 (mppt) cc_final: 0.7127 (ttpp) REVERT: D 77 GLU cc_start: 0.6775 (tp30) cc_final: 0.6379 (tp30) REVERT: D 84 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.5723 (tptt) REVERT: D 130 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7344 (mm) REVERT: H 283 GLN cc_start: 0.5749 (OUTLIER) cc_final: 0.5478 (pm20) outliers start: 35 outliers final: 17 residues processed: 245 average time/residue: 0.1096 time to fit residues: 38.5470 Evaluate side-chains 228 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 C residue 55 VAL 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 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: 1.9990 chunk 58 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 68 optimal weight: 0.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.164295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143055 restraints weight = 21365.306| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.31 r_work: 0.3743 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13340 Z= 0.146 Angle : 0.579 8.002 18234 Z= 0.312 Chirality : 0.043 0.382 2052 Planarity : 0.004 0.046 2120 Dihedral : 15.396 174.715 2468 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Rotamer: Outliers : 2.81 % Allowed : 16.13 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.22), residues: 1422 helix: 0.86 (0.23), residues: 543 sheet: -0.98 (0.31), residues: 281 loop : -1.67 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.021 0.001 TYR H 226 PHE 0.025 0.001 PHE D 120 TRP 0.003 0.001 TRP B 52 HIS 0.004 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00322 (13340) covalent geometry : angle 0.57906 (18234) hydrogen bonds : bond 0.04299 ( 548) hydrogen bonds : angle 5.26308 ( 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 265 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: G 91 ILE cc_start: 0.6547 (mm) cc_final: 0.6293 (mm) REVERT: G 140 GLU cc_start: 0.7995 (pm20) cc_final: 0.7783 (pm20) REVERT: F 159 GLU cc_start: 0.5698 (tm-30) cc_final: 0.5414 (tm-30) REVERT: F 171 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7287 (mtpt) REVERT: C 22 LYS cc_start: 0.5090 (mmtt) cc_final: 0.4797 (mmtt) REVERT: C 63 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.7012 (t80) REVERT: C 73 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6458 (tp30) REVERT: C 118 LYS cc_start: 0.8019 (mppt) cc_final: 0.7128 (ttpp) REVERT: D 77 GLU cc_start: 0.6742 (tp30) cc_final: 0.6301 (tp30) REVERT: D 130 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7296 (mm) REVERT: H 283 GLN cc_start: 0.5774 (OUTLIER) cc_final: 0.5508 (pm20) outliers start: 36 outliers final: 22 residues processed: 251 average time/residue: 0.0899 time to fit residues: 33.2322 Evaluate side-chains 232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE 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 30 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 179 MET 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 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: 0.9990 chunk 145 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS G 97 GLN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN 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 = 0.4095 r_free = 0.4095 target = 0.163247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141186 restraints weight = 21661.081| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.39 r_work: 0.3706 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13340 Z= 0.172 Angle : 0.596 9.506 18234 Z= 0.320 Chirality : 0.044 0.392 2052 Planarity : 0.004 0.047 2120 Dihedral : 15.364 174.231 2468 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.68 % Favored : 92.97 % Rotamer: Outliers : 2.96 % Allowed : 18.16 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.22), residues: 1422 helix: 0.82 (0.23), residues: 541 sheet: -1.08 (0.31), residues: 279 loop : -1.62 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 64 TYR 0.023 0.001 TYR F 180 PHE 0.035 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 covalent geometry : bond 0.00382 (13340) covalent geometry : angle 0.59578 (18234) hydrogen bonds : bond 0.04366 ( 548) hydrogen bonds : angle 5.29042 ( 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 247 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: G 91 ILE cc_start: 0.6630 (mm) cc_final: 0.6392 (mm) REVERT: F 159 GLU cc_start: 0.5678 (tm-30) cc_final: 0.5461 (tm-30) REVERT: F 171 LYS cc_start: 0.7432 (mtpt) cc_final: 0.7217 (mtpt) REVERT: C 22 LYS cc_start: 0.5093 (mmtt) cc_final: 0.4795 (mmtt) REVERT: C 63 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.7030 (t80) REVERT: C 118 LYS cc_start: 0.8024 (mppt) cc_final: 0.7124 (ttpp) REVERT: D 77 GLU cc_start: 0.6765 (tp30) cc_final: 0.6354 (tp30) REVERT: D 130 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7256 (mm) REVERT: B 158 GLU cc_start: 0.8125 (tp30) cc_final: 0.7864 (tp30) REVERT: H 198 GLU cc_start: 0.6987 (mp0) cc_final: 0.6384 (pm20) REVERT: H 283 GLN cc_start: 0.5722 (OUTLIER) cc_final: 0.5440 (pm20) outliers start: 38 outliers final: 26 residues processed: 233 average time/residue: 0.0950 time to fit residues: 32.4100 Evaluate side-chains 229 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 197 THR 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 63 PHE 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 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 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: 2.9990 chunk 111 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS G 97 GLN C 41 ASN C 71 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN 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 = 0.4104 r_free = 0.4104 target = 0.164046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.142268 restraints weight = 21400.984| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.34 r_work: 0.3722 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13340 Z= 0.153 Angle : 0.589 8.391 18234 Z= 0.315 Chirality : 0.044 0.386 2052 Planarity : 0.004 0.046 2120 Dihedral : 15.361 174.667 2468 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.40 % Favored : 93.18 % Rotamer: Outliers : 3.51 % Allowed : 18.16 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.22), residues: 1422 helix: 0.88 (0.23), residues: 541 sheet: -1.07 (0.31), residues: 278 loop : -1.64 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.023 0.001 TYR F 180 PHE 0.027 0.001 PHE D 120 TRP 0.004 0.001 TRP H 230 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00340 (13340) covalent geometry : angle 0.58916 (18234) hydrogen bonds : bond 0.04250 ( 548) hydrogen bonds : angle 5.21528 ( 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 256 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: G 91 ILE cc_start: 0.6595 (mm) cc_final: 0.6383 (mm) REVERT: G 138 GLN cc_start: 0.7917 (tt0) cc_final: 0.7496 (mt0) REVERT: F 159 GLU cc_start: 0.5605 (tm-30) cc_final: 0.5377 (tm-30) REVERT: F 171 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7214 (mtpt) REVERT: C 22 LYS cc_start: 0.5094 (mmtt) cc_final: 0.4810 (mmtt) REVERT: C 63 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7117 (t80) REVERT: C 88 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: C 118 LYS cc_start: 0.8018 (mppt) cc_final: 0.7115 (ttpp) REVERT: D 63 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: D 72 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 77 GLU cc_start: 0.6764 (tp30) cc_final: 0.6314 (tp30) REVERT: D 130 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7320 (mm) REVERT: B 158 GLU cc_start: 0.8188 (tp30) cc_final: 0.7879 (tp30) REVERT: B 226 MET cc_start: 0.6276 (tpp) cc_final: 0.6032 (tpp) REVERT: H 198 GLU cc_start: 0.6956 (mp0) cc_final: 0.6375 (pm20) REVERT: H 283 GLN cc_start: 0.5712 (OUTLIER) cc_final: 0.5444 (pm20) outliers start: 45 outliers final: 27 residues processed: 241 average time/residue: 0.1006 time to fit residues: 35.4262 Evaluate side-chains 232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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 155 ASN Chi-restraints excluded: chain G residue 197 THR 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 63 PHE Chi-restraints excluded: chain C residue 88 GLU 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 44 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS G 18 HIS G 97 GLN C 41 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 207 GLN H 114 ASN H 148 ASN ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.159831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137567 restraints weight = 21711.839| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.39 r_work: 0.3660 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13340 Z= 0.237 Angle : 0.660 8.544 18234 Z= 0.352 Chirality : 0.046 0.418 2052 Planarity : 0.005 0.117 2120 Dihedral : 15.452 173.203 2468 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.88 % Favored : 91.70 % Rotamer: Outliers : 3.35 % Allowed : 18.94 % Favored : 77.71 % 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 aren not related in a simple way. whole: -1.02 (0.22), residues: 1422 helix: 0.83 (0.23), residues: 530 sheet: -1.29 (0.31), residues: 276 loop : -1.70 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 64 TYR 0.025 0.002 TYR F 180 PHE 0.023 0.002 PHE D 120 TRP 0.011 0.002 TRP H 230 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00533 (13340) covalent geometry : angle 0.66033 (18234) hydrogen bonds : bond 0.04661 ( 548) hydrogen bonds : angle 5.45598 ( 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 246 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 42 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8510 (ttpt) REVERT: F 147 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: F 171 LYS cc_start: 0.7521 (mtpt) cc_final: 0.7264 (mtpt) REVERT: C 22 LYS cc_start: 0.5074 (mmtt) cc_final: 0.4791 (mmtt) REVERT: C 63 PHE cc_start: 0.7298 (OUTLIER) cc_final: 0.7003 (t80) REVERT: C 118 LYS cc_start: 0.8048 (mppt) cc_final: 0.7132 (ttpp) REVERT: D 63 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: D 77 GLU cc_start: 0.6875 (tp30) cc_final: 0.6481 (tp30) REVERT: D 130 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7159 (mm) REVERT: B 129 GLN cc_start: 0.7797 (mt0) cc_final: 0.7363 (mt0) REVERT: B 158 GLU cc_start: 0.8195 (tp30) cc_final: 0.7595 (tp30) REVERT: H 198 GLU cc_start: 0.7002 (mp0) cc_final: 0.6412 (pm20) REVERT: H 224 LYS cc_start: 0.7716 (tttt) cc_final: 0.6848 (tmtt) REVERT: H 283 GLN cc_start: 0.5513 (OUTLIER) cc_final: 0.5186 (pm20) outliers start: 43 outliers final: 32 residues processed: 231 average time/residue: 0.1126 time to fit residues: 37.0241 Evaluate side-chains 228 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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 G residue 155 ASN 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 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain F residue 209 THR 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS G 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 H 324 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.162967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141071 restraints weight = 21421.778| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.34 r_work: 0.3707 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13340 Z= 0.158 Angle : 0.611 8.733 18234 Z= 0.327 Chirality : 0.044 0.399 2052 Planarity : 0.004 0.080 2120 Dihedral : 15.436 174.944 2468 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.68 % Favored : 92.97 % Rotamer: Outliers : 3.35 % Allowed : 19.33 % Favored : 77.32 % 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 aren not related in a simple way. whole: -0.96 (0.22), residues: 1422 helix: 0.82 (0.23), residues: 541 sheet: -1.20 (0.31), residues: 273 loop : -1.68 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 52 TYR 0.023 0.001 TYR F 180 PHE 0.022 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 covalent geometry : bond 0.00355 (13340) covalent geometry : angle 0.61083 (18234) hydrogen bonds : bond 0.04293 ( 548) hydrogen bonds : angle 5.29801 ( 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 254 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7539 (mt-10) REVERT: G 6 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7584 (ptpp) REVERT: G 138 GLN cc_start: 0.7927 (tt0) cc_final: 0.7513 (mt0) REVERT: F 147 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: F 171 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7261 (mtpt) REVERT: C 22 LYS cc_start: 0.5069 (mmtt) cc_final: 0.4798 (mmtt) REVERT: C 63 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 88 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: C 118 LYS cc_start: 0.8012 (mppt) cc_final: 0.7118 (ttpp) REVERT: D 63 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: D 77 GLU cc_start: 0.6835 (tp30) cc_final: 0.6402 (tp30) REVERT: D 130 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7309 (mm) REVERT: B 129 GLN cc_start: 0.7759 (mt0) cc_final: 0.7320 (mt0) REVERT: B 158 GLU cc_start: 0.8172 (tp30) cc_final: 0.7633 (tp30) REVERT: H 198 GLU cc_start: 0.6988 (mp0) cc_final: 0.6399 (pm20) REVERT: H 224 LYS cc_start: 0.7710 (tttt) cc_final: 0.6871 (tmtt) REVERT: H 283 GLN cc_start: 0.5553 (OUTLIER) cc_final: 0.5250 (pm20) outliers start: 43 outliers final: 27 residues processed: 242 average time/residue: 0.1143 time to fit residues: 39.8970 Evaluate side-chains 231 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 81 ARG Chi-restraints excluded: chain F residue 103 PHE 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 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 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 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=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: 1.9990 chunk 10 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 0.0020 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.162204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140133 restraints weight = 21574.118| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.36 r_work: 0.3692 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13340 Z= 0.184 Angle : 0.644 11.545 18234 Z= 0.340 Chirality : 0.045 0.403 2052 Planarity : 0.004 0.052 2120 Dihedral : 15.427 174.264 2468 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.31 % Favored : 92.33 % Rotamer: Outliers : 2.96 % Allowed : 19.88 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.22), residues: 1422 helix: 0.81 (0.23), residues: 535 sheet: -1.45 (0.30), residues: 286 loop : -1.57 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 64 TYR 0.025 0.002 TYR F 180 PHE 0.024 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 covalent geometry : bond 0.00417 (13340) covalent geometry : angle 0.64416 (18234) hydrogen bonds : bond 0.04395 ( 548) hydrogen bonds : angle 5.32395 ( 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 236 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 6 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7585 (ptpp) REVERT: F 42 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8561 (ttpt) REVERT: F 147 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: F 171 LYS cc_start: 0.7552 (mtpt) cc_final: 0.7305 (mtpt) REVERT: C 22 LYS cc_start: 0.5101 (mmtt) cc_final: 0.4842 (mmtt) REVERT: C 63 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7027 (t80) REVERT: C 118 LYS cc_start: 0.8017 (mppt) cc_final: 0.7119 (ttpp) REVERT: D 63 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: D 77 GLU cc_start: 0.6856 (tp30) cc_final: 0.6418 (tp30) REVERT: D 97 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7292 (mm-30) REVERT: D 130 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7326 (mm) REVERT: B 129 GLN cc_start: 0.7762 (mt0) cc_final: 0.7330 (mt0) REVERT: B 158 GLU cc_start: 0.8146 (tp30) cc_final: 0.7584 (tp30) REVERT: B 226 MET cc_start: 0.5910 (tpp) cc_final: 0.5508 (mpp) REVERT: H 198 GLU cc_start: 0.7071 (mp0) cc_final: 0.6450 (pm20) REVERT: H 283 GLN cc_start: 0.5438 (OUTLIER) cc_final: 0.5126 (pm20) outliers start: 38 outliers final: 27 residues processed: 226 average time/residue: 0.1223 time to fit residues: 39.7710 Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 97 GLN Chi-restraints excluded: chain F residue 103 PHE 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 109 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 75 optimal weight: 0.0570 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS G 97 GLN F 97 GLN F 155 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN ** H 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.165674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143948 restraints weight = 21604.189| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.38 r_work: 0.3746 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13340 Z= 0.136 Angle : 0.623 11.593 18234 Z= 0.327 Chirality : 0.044 0.379 2052 Planarity : 0.004 0.050 2120 Dihedral : 15.414 175.489 2468 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.47 % Favored : 93.18 % Rotamer: Outliers : 2.73 % Allowed : 20.50 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.22), residues: 1422 helix: 0.92 (0.23), residues: 537 sheet: -1.25 (0.31), residues: 281 loop : -1.65 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.023 0.001 TYR F 180 PHE 0.022 0.002 PHE D 16 TRP 0.005 0.001 TRP B 301 HIS 0.003 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00301 (13340) covalent geometry : angle 0.62319 (18234) hydrogen bonds : bond 0.04172 ( 548) hydrogen bonds : angle 5.19358 ( 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 251 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7399 (mt-10) REVERT: G 6 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7585 (ptpp) REVERT: G 138 GLN cc_start: 0.7932 (tt0) cc_final: 0.7545 (mt0) REVERT: F 42 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8544 (ttpt) REVERT: F 147 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: F 171 LYS cc_start: 0.7403 (mtpt) cc_final: 0.7142 (mtpt) REVERT: C 22 LYS cc_start: 0.5170 (mmtt) cc_final: 0.4921 (mmtt) REVERT: C 63 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.7042 (t80) REVERT: C 88 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: C 118 LYS cc_start: 0.7991 (mppt) cc_final: 0.7108 (ttpp) REVERT: D 63 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: D 77 GLU cc_start: 0.6805 (tp30) cc_final: 0.6359 (tp30) REVERT: D 130 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7358 (mm) REVERT: B 129 GLN cc_start: 0.7736 (mt0) cc_final: 0.7295 (mt0) REVERT: B 158 GLU cc_start: 0.8142 (tp30) cc_final: 0.7605 (tp30) REVERT: B 226 MET cc_start: 0.5756 (tpp) cc_final: 0.5387 (mpp) REVERT: H 198 GLU cc_start: 0.7023 (mp0) cc_final: 0.6396 (pm20) REVERT: H 283 GLN cc_start: 0.5511 (OUTLIER) cc_final: 0.5192 (pm20) outliers start: 35 outliers final: 23 residues processed: 242 average time/residue: 0.1199 time to fit residues: 41.3318 Evaluate side-chains 228 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 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 97 GLN Chi-restraints excluded: chain F residue 103 PHE 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 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 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 220 ILE Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 57 optimal weight: 0.6980 chunk 66 optimal weight: 0.0000 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS F 97 GLN F 155 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 60 GLN H 148 ASN H 324 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140052 restraints weight = 21563.915| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.37 r_work: 0.3693 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13340 Z= 0.197 Angle : 0.667 11.122 18234 Z= 0.351 Chirality : 0.046 0.396 2052 Planarity : 0.004 0.061 2120 Dihedral : 15.401 173.914 2468 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.45 % Favored : 92.19 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.22), residues: 1422 helix: 0.82 (0.23), residues: 537 sheet: -1.32 (0.31), residues: 282 loop : -1.66 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.026 0.002 TYR D 133 PHE 0.022 0.002 PHE D 16 TRP 0.006 0.001 TRP H 230 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00445 (13340) covalent geometry : angle 0.66673 (18234) hydrogen bonds : bond 0.04387 ( 548) hydrogen bonds : angle 5.32496 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.35 seconds wall clock time: 45 minutes 24.25 seconds (2724.25 seconds total)