Starting phenix.real_space_refine on Sat Sep 12 02:29:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.map" model { file = "/net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do6_27593/09_2026/8do6_27593.cif" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12980 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNAv2': 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: {'RNAv2': 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: 2.52, per 1000 atoms: 0.19 Number of scatterers: 12980 At special positions: 0 Unit cell: (93.906, 95.598, 164.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 61 15.00 O 2667 8.00 N 2198 7.00 C 8030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 392.2 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 20 sheets defined 40.8% alpha, 21.7% beta 17 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.48 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: 1.77 Time building geometry restraints manager: 1.27 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: 18189 4.90 - 9.80: 41 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=" CB GLU B 158 " pdb=" CG GLU B 158 " pdb=" CD GLU B 158 " ideal model delta sigma weight residual 112.60 118.29 -5.69 1.70e+00 3.46e-01 1.12e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6674 17.98 - 35.95: 890 35.95 - 53.93: 222 53.93 - 71.90: 87 71.90 - 89.88: 26 Dihedral angle restraints: 7899 sinusoidal: 3701 harmonic: 4198 Sorted by residual: dihedral pdb=" C4' U I 26 " pdb=" C3' U I 26 " pdb=" C2' U I 26 " pdb=" C1' U I 26 " ideal model delta sinusoidal sigma weight residual 36.34 -37.08 73.42 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' G I 15 " pdb=" C3' G I 15 " pdb=" C2' G I 15 " pdb=" C1' G I 15 " ideal model delta sinusoidal sigma weight residual 36.34 -36.97 73.31 1 3.10e+00 1.04e-01 7.12e+02 dihedral pdb=" C4' G I 3 " pdb=" C3' G I 3 " pdb=" C2' G I 3 " pdb=" C1' G I 3 " ideal model delta sinusoidal sigma weight residual 36.34 -36.87 73.21 1 3.10e+00 1.04e-01 7.10e+02 ... (remaining 7896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1710 0.064 - 0.128: 224 0.128 - 0.192: 21 0.192 - 0.256: 70 0.256 - 0.319: 27 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C3' A I 27 " pdb=" C4' A I 27 " pdb=" O3' A I 27 " pdb=" C2' A I 27 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C3' G I 21 " pdb=" C4' G I 21 " pdb=" O3' G I 21 " pdb=" C2' G I 21 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' G I 15 " pdb=" C4' G I 15 " pdb=" O3' G I 15 " pdb=" C2' G I 15 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.21e+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: 3.940 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.438 13340 Z= 0.194 Angle : 0.771 24.509 18234 Z= 0.391 Chirality : 0.067 0.319 2052 Planarity : 0.005 0.085 2120 Dihedral : 18.099 89.877 5207 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.33 % Favored : 93.25 % Rotamer: Outliers : 0.62 % Allowed : 13.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1422 helix: 0.38 (0.23), residues: 526 sheet: -1.20 (0.30), residues: 297 loop : -1.60 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 64 TYR 0.022 0.002 TYR C 87 PHE 0.019 0.002 PHE D 74 TRP 0.005 0.001 TRP H 230 HIS 0.005 0.001 HIS H 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.19 (13340) covalent geometry : angle 0.77064 / 0.39 (18234) hydrogen bonds : bond 0.16554 / 11.31 ( 548) hydrogen bonds : angle 7.19373 / 5.01 ( 1572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.440 Fit side-chains REVERT: D 110 ARG cc_start: 0.6254 (mtm180) cc_final: 0.6001 (mtp180) REVERT: B 226 MET cc_start: 0.5894 (tpp) cc_final: 0.5360 (mpp) REVERT: B 283 PHE cc_start: 0.7613 (m-80) cc_final: 0.7367 (m-80) REVERT: H 85 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7656 (pttp) REVERT: H 186 MET cc_start: 0.7880 (tpp) cc_final: 0.7095 (tpp) outliers start: 8 outliers final: 3 residues processed: 222 average time/residue: 0.1104 time to fit residues: 35.9297 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 : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain B residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 74 GLN E 110 HIS G 57 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.169649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149130 restraints weight = 21285.990| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.29 r_work: 0.3830 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13340 Z= 0.158 Angle : 0.891 18.725 18234 Z= 0.405 Chirality : 0.082 1.409 2052 Planarity : 0.004 0.055 2120 Dihedral : 12.528 136.916 2296 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Rotamer: Outliers : 2.03 % Allowed : 13.64 % Favored : 84.33 % 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 are not related in a simple way. whole: -0.84 (0.22), residues: 1422 helix: 0.85 (0.23), residues: 540 sheet: -1.12 (0.30), residues: 296 loop : -1.55 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 137 TYR 0.026 0.001 TYR H 226 PHE 0.017 0.001 PHE D 74 TRP 0.004 0.001 TRP B 52 HIS 0.004 0.001 HIS F 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (13340) covalent geometry : angle 0.89079 / 0.40 (18234) hydrogen bonds : bond 0.05073 / 3.61 ( 548) hydrogen bonds : angle 5.65143 / 3.93 ( 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 277 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6905 (mt-10) REVERT: D 26 LYS cc_start: 0.6229 (pptt) cc_final: 0.6005 (pptt) REVERT: D 88 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7074 (mp0) REVERT: B 158 GLU cc_start: 0.7760 (mp0) cc_final: 0.7528 (mp0) REVERT: B 226 MET cc_start: 0.5901 (tpp) cc_final: 0.5162 (mpp) REVERT: H 186 MET cc_start: 0.7880 (tpp) cc_final: 0.7433 (mmt) REVERT: H 283 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5753 (pm20) outliers start: 26 outliers final: 11 residues processed: 266 average time/residue: 0.1191 time to fit residues: 45.6838 Evaluate side-chains 221 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 164 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 283 GLN 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: 0.7980 chunk 19 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 73 optimal weight: 0.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN C 71 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.168572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147728 restraints weight = 21352.011| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.31 r_work: 0.3807 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13340 Z= 0.163 Angle : 0.798 15.129 18234 Z= 0.374 Chirality : 0.070 1.147 2052 Planarity : 0.004 0.058 2120 Dihedral : 12.190 140.215 2290 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.19 % Favored : 93.46 % Rotamer: Outliers : 2.10 % Allowed : 14.81 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.22), residues: 1422 helix: 0.89 (0.23), residues: 538 sheet: -1.12 (0.30), residues: 304 loop : -1.68 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 137 TYR 0.015 0.001 TYR C 87 PHE 0.031 0.001 PHE D 120 TRP 0.004 0.001 TRP H 230 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (13340) covalent geometry : angle 0.79761 / 0.37 (18234) hydrogen bonds : bond 0.04623 / 3.27 ( 548) hydrogen bonds : angle 5.41511 / 3.79 ( 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 264 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7052 (mt-10) REVERT: F 144 ARG cc_start: 0.8352 (ptm-80) cc_final: 0.8115 (ptm160) REVERT: F 159 GLU cc_start: 0.5540 (tm-30) cc_final: 0.5328 (tm-30) REVERT: F 171 LYS cc_start: 0.7442 (mtpt) cc_final: 0.7159 (mtpt) REVERT: C 22 LYS cc_start: 0.5157 (mmtt) cc_final: 0.4842 (mmtt) REVERT: C 91 ARG cc_start: 0.6008 (ptm160) cc_final: 0.5699 (ptm160) REVERT: C 118 LYS cc_start: 0.8012 (mppt) cc_final: 0.7133 (ttpp) REVERT: D 130 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7377 (mm) REVERT: B 226 MET cc_start: 0.6069 (tpp) cc_final: 0.5497 (tpp) REVERT: H 283 GLN cc_start: 0.6004 (OUTLIER) cc_final: 0.5781 (pm20) outliers start: 27 outliers final: 14 residues processed: 254 average time/residue: 0.1133 time to fit residues: 42.2889 Evaluate side-chains 232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain C residue 55 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 138 GLU Chi-restraints excluded: chain B residue 164 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 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 52 optimal weight: 0.3980 chunk 58 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.0170 chunk 68 optimal weight: 9.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** F 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 60 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 = 0.4143 r_free = 0.4143 target = 0.166582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145734 restraints weight = 21224.222| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.28 r_work: 0.3785 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13340 Z= 0.177 Angle : 0.789 16.589 18234 Z= 0.372 Chirality : 0.064 0.737 2052 Planarity : 0.004 0.060 2120 Dihedral : 12.237 139.908 2290 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.54 % Favored : 93.11 % Rotamer: Outliers : 2.96 % Allowed : 16.21 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1422 helix: 0.88 (0.23), residues: 535 sheet: -1.06 (0.31), residues: 287 loop : -1.60 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.020 0.001 TYR F 180 PHE 0.033 0.002 PHE D 120 TRP 0.005 0.001 TRP H 230 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (13340) covalent geometry : angle 0.78867 / 0.37 (18234) hydrogen bonds : bond 0.04548 / 3.20 ( 548) hydrogen bonds : angle 5.34725 / 3.74 ( 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 263 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 91 ILE cc_start: 0.8782 (tp) cc_final: 0.8580 (tp) REVERT: E 124 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: F 159 GLU cc_start: 0.5676 (tm-30) cc_final: 0.5408 (tm-30) REVERT: F 171 LYS cc_start: 0.7473 (mtpt) cc_final: 0.7223 (mtpt) REVERT: F 180 TYR cc_start: 0.7917 (p90) cc_final: 0.7716 (p90) REVERT: C 22 LYS cc_start: 0.5180 (mmtt) cc_final: 0.4883 (mmtt) REVERT: C 63 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.7007 (t80) REVERT: C 118 LYS cc_start: 0.8033 (mppt) cc_final: 0.7146 (ttpp) REVERT: D 77 GLU cc_start: 0.6705 (tp30) cc_final: 0.6275 (tp30) REVERT: D 130 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7176 (mm) REVERT: H 283 GLN cc_start: 0.5841 (OUTLIER) cc_final: 0.5586 (pm20) outliers start: 38 outliers final: 21 residues processed: 249 average time/residue: 0.1168 time to fit residues: 42.7436 Evaluate side-chains 235 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 97 GLN 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 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 H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 28 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN 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 = 0.4145 r_free = 0.4145 target = 0.167251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.145846 restraints weight = 21428.936| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.35 r_work: 0.3774 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13340 Z= 0.165 Angle : 0.762 15.294 18234 Z= 0.361 Chirality : 0.061 0.513 2052 Planarity : 0.004 0.071 2120 Dihedral : 12.254 139.541 2290 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.12 % Favored : 93.60 % Rotamer: Outliers : 3.20 % Allowed : 16.68 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.22), residues: 1422 helix: 0.90 (0.23), residues: 542 sheet: -1.09 (0.31), residues: 287 loop : -1.61 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 64 TYR 0.017 0.001 TYR F 180 PHE 0.025 0.001 PHE D 120 TRP 0.004 0.001 TRP H 230 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (13340) covalent geometry : angle 0.76155 / 0.36 (18234) hydrogen bonds : bond 0.04481 / 3.16 ( 548) hydrogen bonds : angle 5.25037 / 3.68 ( 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 260 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: G 27 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6520 (ttt) REVERT: G 138 GLN cc_start: 0.7827 (tt0) cc_final: 0.7282 (mt0) REVERT: F 144 ARG cc_start: 0.8407 (ptm-80) cc_final: 0.8170 (ptm160) REVERT: F 159 GLU cc_start: 0.5601 (tm-30) cc_final: 0.5396 (tm-30) REVERT: F 171 LYS cc_start: 0.7401 (mtpt) cc_final: 0.7163 (mtpt) REVERT: F 180 TYR cc_start: 0.8073 (p90) cc_final: 0.7690 (p90) REVERT: C 22 LYS cc_start: 0.5132 (mmtt) cc_final: 0.4848 (mmtt) REVERT: C 63 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7093 (t80) REVERT: C 86 TYR cc_start: 0.7518 (m-80) cc_final: 0.7299 (m-80) REVERT: C 88 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: C 118 LYS cc_start: 0.7980 (mppt) cc_final: 0.7107 (ttpp) REVERT: D 77 GLU cc_start: 0.6731 (tp30) cc_final: 0.6257 (tp30) REVERT: D 130 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7194 (mm) REVERT: H 283 GLN cc_start: 0.5783 (OUTLIER) cc_final: 0.5519 (pm20) outliers start: 41 outliers final: 25 residues processed: 245 average time/residue: 0.1127 time to fit residues: 40.4022 Evaluate side-chains 231 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 32 ASP 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 C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 88 GLU 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 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 134 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: 1.9990 chunk 111 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 0.0040 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN C 41 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 207 GLN H 148 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.164658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143017 restraints weight = 21289.491| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.33 r_work: 0.3739 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2391 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= 0.198 Angle : 0.794 15.436 18234 Z= 0.378 Chirality : 0.063 0.534 2052 Planarity : 0.004 0.077 2120 Dihedral : 12.372 144.577 2290 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 3.43 % Allowed : 18.16 % Favored : 78.41 % 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 are not related in a simple way. whole: -0.90 (0.22), residues: 1422 helix: 0.85 (0.23), residues: 543 sheet: -1.20 (0.30), residues: 287 loop : -1.62 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.016 0.002 TYR F 180 PHE 0.020 0.002 PHE D 120 TRP 0.008 0.001 TRP H 230 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (13340) covalent geometry : angle 0.79444 / 0.38 (18234) hydrogen bonds : bond 0.04580 / 3.21 ( 548) hydrogen bonds : angle 5.32601 / 3.74 ( 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 253 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 81 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7622 (ptp-170) REVERT: F 159 GLU cc_start: 0.5623 (tm-30) cc_final: 0.5414 (tm-30) REVERT: F 171 LYS cc_start: 0.7504 (mtpt) cc_final: 0.7280 (mtpt) REVERT: C 22 LYS cc_start: 0.5116 (mmtt) cc_final: 0.4837 (mmtt) REVERT: C 63 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7118 (t80) REVERT: C 118 LYS cc_start: 0.8007 (mppt) cc_final: 0.7108 (ttpp) REVERT: D 63 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: D 77 GLU cc_start: 0.6760 (tp30) cc_final: 0.6309 (tp30) REVERT: D 130 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7150 (mm) REVERT: H 186 MET cc_start: 0.7923 (tpp) cc_final: 0.7036 (mmt) REVERT: H 198 GLU cc_start: 0.7003 (mp0) cc_final: 0.6407 (pm20) REVERT: H 283 GLN cc_start: 0.5719 (OUTLIER) cc_final: 0.5416 (pm20) outliers start: 44 outliers final: 26 residues processed: 237 average time/residue: 0.1094 time to fit residues: 37.4814 Evaluate side-chains 222 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 158 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 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 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 134 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 44 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 HIS G 97 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 214 GLN H 114 ASN H 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136725 restraints weight = 21764.408| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.32 r_work: 0.3648 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 13340 Z= 0.328 Angle : 0.934 16.155 18234 Z= 0.445 Chirality : 0.072 0.636 2052 Planarity : 0.005 0.086 2120 Dihedral : 13.016 152.323 2290 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.51 % Favored : 91.07 % Rotamer: Outliers : 3.66 % Allowed : 19.10 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.21), residues: 1422 helix: 0.61 (0.22), residues: 528 sheet: -1.67 (0.30), residues: 278 loop : -1.68 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 91 TYR 0.035 0.002 TYR H 223 PHE 0.025 0.002 PHE D 120 TRP 0.014 0.002 TRP H 230 HIS 0.009 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.33 (13340) covalent geometry : angle 0.93446 / 0.45 (18234) hydrogen bonds : bond 0.05297 / 3.67 ( 548) hydrogen bonds : angle 5.73103 / 4.03 ( 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 257 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: F 42 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8502 (ttpt) REVERT: F 81 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7610 (ptp-170) REVERT: F 147 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: F 159 GLU cc_start: 0.5737 (tm-30) cc_final: 0.5339 (tm-30) REVERT: F 171 LYS cc_start: 0.7521 (mtpt) cc_final: 0.7277 (mtpt) REVERT: C 118 LYS cc_start: 0.8078 (mppt) cc_final: 0.7177 (ttpp) REVERT: D 63 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: D 77 GLU cc_start: 0.6857 (tp30) cc_final: 0.6461 (tp30) REVERT: D 97 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7444 (mm-30) REVERT: D 130 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7223 (mm) REVERT: B 158 GLU cc_start: 0.7821 (mp0) cc_final: 0.7582 (mp0) REVERT: H 28 ASP cc_start: 0.8315 (t0) cc_final: 0.7922 (t0) REVERT: H 186 MET cc_start: 0.7958 (tpp) cc_final: 0.7715 (tpp) REVERT: H 198 GLU cc_start: 0.7162 (mp0) cc_final: 0.6547 (pm20) REVERT: H 283 GLN cc_start: 0.5501 (OUTLIER) cc_final: 0.5237 (pm20) REVERT: H 290 THR cc_start: 0.7021 (m) cc_final: 0.6669 (p) outliers start: 47 outliers final: 28 residues processed: 243 average time/residue: 0.1248 time to fit residues: 43.3084 Evaluate side-chains 229 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 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 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 153 ILE 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 158 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 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 134 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 171 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 131 optimal weight: 0.0170 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 128 ASN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 214 GLN H 148 ASN H 324 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.165331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.143855 restraints weight = 21258.435| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.34 r_work: 0.3751 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13340 Z= 0.162 Angle : 0.799 14.976 18234 Z= 0.381 Chirality : 0.062 0.465 2052 Planarity : 0.004 0.083 2120 Dihedral : 12.618 145.913 2290 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.40 % Favored : 93.18 % Rotamer: Outliers : 3.27 % Allowed : 20.03 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1422 helix: 0.73 (0.22), residues: 541 sheet: -1.62 (0.29), residues: 289 loop : -1.53 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 52 TYR 0.032 0.002 TYR H 223 PHE 0.030 0.002 PHE C 63 TRP 0.004 0.001 TRP H 230 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (13340) covalent geometry : angle 0.79880 / 0.38 (18234) hydrogen bonds : bond 0.04557 / 3.24 ( 548) hydrogen bonds : angle 5.40316 / 3.79 ( 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 264 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: G 6 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7584 (ptpp) REVERT: G 27 MET cc_start: 0.6938 (ttt) cc_final: 0.6649 (ttt) REVERT: G 138 GLN cc_start: 0.7986 (tt0) cc_final: 0.7368 (mt0) REVERT: F 27 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.5128 (tpt) REVERT: F 81 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (ptp-170) REVERT: F 147 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: F 171 LYS cc_start: 0.7428 (mtpt) cc_final: 0.7193 (mtpt) REVERT: F 180 TYR cc_start: 0.8044 (p90) cc_final: 0.7582 (p90) REVERT: C 22 LYS cc_start: 0.5086 (mmtt) cc_final: 0.4808 (mmtt) REVERT: C 118 LYS cc_start: 0.8033 (mppt) cc_final: 0.7132 (ttpp) REVERT: C 128 GLU cc_start: 0.6920 (tt0) cc_final: 0.6328 (tt0) REVERT: D 63 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: D 77 GLU cc_start: 0.6815 (tp30) cc_final: 0.6339 (tp30) REVERT: D 84 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.5593 (tptt) REVERT: D 97 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7359 (mm-30) REVERT: D 130 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7321 (mm) REVERT: B 65 TYR cc_start: 0.7447 (p90) cc_final: 0.6399 (p90) REVERT: B 129 GLN cc_start: 0.7746 (mt0) cc_final: 0.7469 (mt0) REVERT: B 158 GLU cc_start: 0.7804 (mp0) cc_final: 0.7494 (mp0) REVERT: B 226 MET cc_start: 0.6100 (tpp) cc_final: 0.5763 (tpp) REVERT: H 28 ASP cc_start: 0.8218 (t0) cc_final: 0.7861 (t0) REVERT: H 198 GLU cc_start: 0.7096 (mp0) cc_final: 0.6479 (pm20) REVERT: H 224 LYS cc_start: 0.7679 (tttt) cc_final: 0.6801 (tmtt) REVERT: H 283 GLN cc_start: 0.5406 (OUTLIER) cc_final: 0.5146 (pm20) outliers start: 42 outliers final: 25 residues processed: 253 average time/residue: 0.1187 time to fit residues: 43.2394 Evaluate side-chains 234 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 27 MET 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 158 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL 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 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 134 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=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: 1.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 155 ASN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.137252 restraints weight = 21590.971| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.36 r_work: 0.3664 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 13340 Z= 0.295 Angle : 0.918 15.930 18234 Z= 0.438 Chirality : 0.070 0.688 2052 Planarity : 0.005 0.086 2120 Dihedral : 13.166 175.964 2290 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.37 % Favored : 91.21 % Rotamer: Outliers : 3.27 % Allowed : 20.65 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.21), residues: 1422 helix: 0.58 (0.22), residues: 530 sheet: -1.75 (0.29), residues: 286 loop : -1.64 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 52 TYR 0.022 0.002 TYR F 180 PHE 0.031 0.002 PHE C 63 TRP 0.013 0.002 TRP H 230 HIS 0.010 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (13340) covalent geometry : angle 0.91783 / 0.44 (18234) hydrogen bonds : bond 0.05097 / 3.56 ( 548) hydrogen bonds : angle 5.64946 / 3.97 ( 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 242 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: G 6 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7505 (ptpp) REVERT: G 193 GLN cc_start: 0.7891 (mm110) cc_final: 0.7632 (mm-40) REVERT: F 42 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8478 (ttpt) REVERT: F 81 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7554 (ptp-170) REVERT: F 147 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: F 171 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7260 (mtpt) REVERT: C 118 LYS cc_start: 0.8049 (mppt) cc_final: 0.7149 (ttpp) REVERT: D 63 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: D 77 GLU cc_start: 0.6877 (tp30) cc_final: 0.6483 (tp30) REVERT: D 97 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7460 (mm-30) REVERT: D 130 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7194 (mm) REVERT: B 129 GLN cc_start: 0.7816 (mt0) cc_final: 0.7548 (mt0) REVERT: B 158 GLU cc_start: 0.7924 (mp0) cc_final: 0.7647 (mp0) REVERT: B 226 MET cc_start: 0.6172 (tpp) cc_final: 0.5886 (tpp) REVERT: H 28 ASP cc_start: 0.8302 (t0) cc_final: 0.7881 (t0) REVERT: H 198 GLU cc_start: 0.7190 (mp0) cc_final: 0.6521 (pm20) REVERT: H 224 LYS cc_start: 0.7766 (tttt) cc_final: 0.6847 (tmtt) REVERT: H 283 GLN cc_start: 0.5414 (OUTLIER) cc_final: 0.5073 (mp10) REVERT: H 290 THR cc_start: 0.7052 (m) cc_final: 0.6730 (p) outliers start: 42 outliers final: 28 residues processed: 232 average time/residue: 0.1248 time to fit residues: 41.1533 Evaluate side-chains 234 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 153 ILE 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 158 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL 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 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 134 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 207 ASP 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: 1.9990 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN F 97 GLN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 214 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 = 0.4122 r_free = 0.4122 target = 0.165089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143730 restraints weight = 21428.199| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.34 r_work: 0.3747 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13340 Z= 0.172 Angle : 0.820 14.862 18234 Z= 0.392 Chirality : 0.062 0.560 2052 Planarity : 0.004 0.082 2120 Dihedral : 12.807 178.434 2290 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.68 % Favored : 92.90 % Rotamer: Outliers : 2.88 % Allowed : 20.81 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1422 helix: 0.75 (0.23), residues: 537 sheet: -1.64 (0.29), residues: 289 loop : -1.62 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.018 0.002 TYR F 180 PHE 0.026 0.002 PHE C 63 TRP 0.004 0.001 TRP H 230 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (13340) covalent geometry : angle 0.81965 / 0.39 (18234) hydrogen bonds : bond 0.04609 / 3.28 ( 548) hydrogen bonds : angle 5.42556 / 3.81 ( 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 247 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: G 6 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7501 (ptpp) REVERT: G 138 GLN cc_start: 0.7938 (tt0) cc_final: 0.7481 (mt0) REVERT: F 42 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8515 (ttpt) REVERT: F 81 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7572 (ptp-170) REVERT: F 147 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: F 171 LYS cc_start: 0.7446 (mtpt) cc_final: 0.7137 (mtpt) REVERT: F 180 TYR cc_start: 0.8072 (p90) cc_final: 0.7792 (p90) REVERT: C 22 LYS cc_start: 0.5076 (mmtt) cc_final: 0.4823 (mmtt) REVERT: C 118 LYS cc_start: 0.8014 (mppt) cc_final: 0.7124 (ttpp) REVERT: D 63 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: D 77 GLU cc_start: 0.6766 (tp30) cc_final: 0.6283 (tp30) REVERT: D 84 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.5652 (tptt) REVERT: D 97 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7437 (mm-30) REVERT: D 130 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7296 (mm) REVERT: B 65 TYR cc_start: 0.7485 (p90) cc_final: 0.6353 (p90) REVERT: B 129 GLN cc_start: 0.7704 (mt0) cc_final: 0.7370 (mt0) REVERT: B 158 GLU cc_start: 0.7880 (mp0) cc_final: 0.7594 (mp0) REVERT: B 226 MET cc_start: 0.6115 (tpp) cc_final: 0.5863 (tpp) REVERT: H 198 GLU cc_start: 0.7144 (mp0) cc_final: 0.6456 (pm20) REVERT: H 224 LYS cc_start: 0.7608 (tttt) cc_final: 0.6741 (tmtt) REVERT: H 283 GLN cc_start: 0.5520 (OUTLIER) cc_final: 0.5160 (mp10) outliers start: 37 outliers final: 26 residues processed: 237 average time/residue: 0.1224 time to fit residues: 41.5555 Evaluate side-chains 237 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 127 ILE 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 158 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL 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 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 134 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 207 ASP 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: 7.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 110 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 155 ASN ** F 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 214 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 = 0.4102 r_free = 0.4102 target = 0.163582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142082 restraints weight = 21429.272| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.35 r_work: 0.3727 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13340 Z= 0.198 Angle : 0.834 15.289 18234 Z= 0.398 Chirality : 0.064 0.602 2052 Planarity : 0.005 0.085 2120 Dihedral : 12.817 176.707 2290 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.17 % Favored : 92.41 % Rotamer: Outliers : 2.81 % Allowed : 20.97 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.22), residues: 1422 helix: 0.75 (0.22), residues: 537 sheet: -1.66 (0.29), residues: 290 loop : -1.60 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 64 TYR 0.023 0.002 TYR D 133 PHE 0.025 0.002 PHE D 120 TRP 0.005 0.001 TRP H 230 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (13340) covalent geometry : angle 0.83354 / 0.40 (18234) hydrogen bonds : bond 0.04644 / 3.28 ( 548) hydrogen bonds : angle 5.43101 / 3.81 ( 1572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2841.23 seconds wall clock time: 49 minutes 56.75 seconds (2996.75 seconds total)