Starting phenix.real_space_refine on Thu May 15 12:27:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do6_27593/05_2025/8do6_27593.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do6_27593/05_2025/8do6_27593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8do6_27593/05_2025/8do6_27593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do6_27593/05_2025/8do6_27593.map" model { file = "/net/cci-nas-00/data/ceres_data/8do6_27593/05_2025/8do6_27593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do6_27593/05_2025/8do6_27593.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12980 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "F" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1613 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 748 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 15, 'rna3p': 19} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 549 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 13} Link IDs: {'rna2p': 3, 'rna3p': 22} Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 926 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 951 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2296 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 1 Chain: "H" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2671 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 1 Time building chain proxies: 8.28, per 1000 atoms: 0.64 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: 3.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.45 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: 3.74 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 1 1.21 - 1.36: 4132 1.36 - 1.51: 4418 1.51 - 1.66: 4745 1.66 - 1.81: 44 Bond restraints: 13340 Sorted by residual: bond pdb=" CG PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 1.503 1.065 0.438 3.40e-02 8.65e+02 1.66e+02 bond pdb=" N PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" CB PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.31e+00 bond pdb=" CB ASN H 147 " pdb=" CG ASN H 147 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.39e+00 bond pdb=" CB GLU B 158 " pdb=" CG GLU B 158 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 ... (remaining 13335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 18200 4.90 - 9.80: 30 9.80 - 14.71: 2 14.71 - 19.61: 1 19.61 - 24.51: 1 Bond angle restraints: 18234 Sorted by residual: angle pdb=" N PRO H 70 " pdb=" CD PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 103.20 78.69 24.51 1.50e+00 4.44e-01 2.67e+02 angle pdb=" CA PRO H 70 " pdb=" CB PRO H 70 " pdb=" CG PRO H 70 " ideal model delta sigma weight residual 104.50 89.09 15.41 1.90e+00 2.77e-01 6.58e+01 angle pdb=" CA PRO H 70 " pdb=" N PRO H 70 " pdb=" CD PRO H 70 " ideal model delta sigma weight residual 112.00 102.87 9.13 1.40e+00 5.10e-01 4.25e+01 angle pdb=" N PRO H 70 " pdb=" CA PRO H 70 " pdb=" CB PRO H 70 " ideal model delta sigma weight residual 102.60 97.16 5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" O4' A I 27 " pdb=" C1' A I 27 " pdb=" N9 A I 27 " ideal model delta sigma weight residual 108.20 114.47 -6.27 1.50e+00 4.44e-01 1.75e+01 ... (remaining 18229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 7718 34.52 - 69.04: 319 69.04 - 103.57: 38 103.57 - 138.09: 1 138.09 - 172.61: 1 Dihedral angle restraints: 8077 sinusoidal: 3879 harmonic: 4198 Sorted by residual: dihedral pdb=" O4' U I 26 " pdb=" C1' U I 26 " pdb=" N1 U I 26 " pdb=" C2 U I 26 " ideal model delta sinusoidal sigma weight residual -128.00 44.61 -172.61 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " pdb=" C2 C I 8 " ideal model delta sinusoidal sigma weight residual -128.00 7.31 -135.31 1 1.70e+01 3.46e-03 5.68e+01 dihedral pdb=" CA SER F 160 " pdb=" C SER F 160 " pdb=" N GLN F 161 " pdb=" CA GLN F 161 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 8074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1738 0.055 - 0.111: 266 0.111 - 0.166: 41 0.166 - 0.222: 4 0.222 - 0.277: 3 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C1' A I 27 " pdb=" O4' A I 27 " pdb=" C2' A I 27 " pdb=" N9 A I 27 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1' G I 21 " pdb=" O4' G I 21 " pdb=" C2' G I 21 " pdb=" N9 G I 21 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU B 211 " pdb=" CB LEU B 211 " pdb=" CD1 LEU B 211 " pdb=" CD2 LEU B 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2049 not shown) Planarity restraints: 2120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " 0.058 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO B 157 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " -0.036 2.00e-02 2.50e+03 1.79e-02 8.82e+00 pdb=" N9 A I 27 " 0.046 2.00e-02 2.50e+03 pdb=" C8 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A I 27 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A I 27 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A I 27 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A I 27 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A I 27 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " -0.037 2.00e-02 2.50e+03 1.70e-02 8.70e+00 pdb=" N9 G I 21 " 0.044 2.00e-02 2.50e+03 pdb=" C8 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G I 21 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G I 21 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G I 21 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G I 21 " 0.004 2.00e-02 2.50e+03 ... (remaining 2117 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 521 2.70 - 3.25: 13278 3.25 - 3.80: 22147 3.80 - 4.35: 29926 4.35 - 4.90: 47743 Nonbonded interactions: 113615 Sorted by model distance: nonbonded pdb=" OP1 U J 15 " pdb=" OG1 THR D 44 " model vdw 2.146 3.040 nonbonded pdb=" OP1 A I 27 " pdb=" OG SER H 132 " model vdw 2.173 3.040 nonbonded pdb=" O PHE D 98 " pdb=" OG1 THR D 102 " model vdw 2.174 3.040 nonbonded pdb=" OP2 A I 1 " pdb=" OG SER B 37 " model vdw 2.181 3.040 nonbonded pdb=" OP1 C I 31 " pdb=" OH TYR H 297 " model vdw 2.184 3.040 ... (remaining 113610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 16 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 136)) selection = (chain 'D' and (resid 16 through 24 or resid 37 through 136)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.210 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.438 13340 Z= 0.190 Angle : 0.679 24.509 18234 Z= 0.368 Chirality : 0.043 0.277 2052 Planarity : 0.005 0.085 2120 Dihedral : 18.001 172.610 5385 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.33 % Favored : 93.25 % Rotamer: Outliers : 0.62 % Allowed : 13.56 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (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 TRP 0.005 0.001 TRP H 230 HIS 0.005 0.001 HIS H 272 PHE 0.019 0.002 PHE D 74 TYR 0.022 0.002 TYR C 87 ARG 0.005 0.000 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.16554 ( 548) hydrogen bonds : angle 7.19373 ( 1572) covalent geometry : bond 0.00507 (13340) covalent geometry : angle 0.67940 (18234) *********************** 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 : 1.333 Fit side-chains REVERT: D 110 ARG cc_start: 0.6254 (mtm180) cc_final: 0.6001 (mtp180) REVERT: B 226 MET cc_start: 0.5894 (tpp) cc_final: 0.5360 (mpp) REVERT: B 283 PHE cc_start: 0.7612 (m-80) cc_final: 0.7367 (m-80) REVERT: H 85 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7656 (pttp) REVERT: H 186 MET cc_start: 0.7880 (tpp) cc_final: 0.7095 (tpp) outliers start: 8 outliers final: 3 residues processed: 222 average time/residue: 0.2496 time to fit residues: 79.7733 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 : 1.368 ------------------------------------------------------------------------------- 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 123 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 18 HIS G 57 ASN F 110 HIS F 125 ASN ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135784 restraints weight = 21407.176| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.29 r_work: 0.3648 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13340 Z= 0.303 Angle : 0.727 8.747 18234 Z= 0.389 Chirality : 0.048 0.412 2052 Planarity : 0.005 0.055 2120 Dihedral : 15.686 172.991 2474 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.09 % Favored : 91.56 % Rotamer: Outliers : 3.04 % Allowed : 14.42 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1422 helix: 0.55 (0.22), residues: 524 sheet: -1.28 (0.30), residues: 279 loop : -1.79 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 230 HIS 0.007 0.001 HIS B 17 PHE 0.030 0.002 PHE G 166 TYR 0.022 0.002 TYR H 226 ARG 0.006 0.001 ARG G 137 Details of bonding type rmsd hydrogen bonds : bond 0.05590 ( 548) hydrogen bonds : angle 5.94252 ( 1572) covalent geometry : bond 0.00678 (13340) covalent geometry : angle 0.72705 (18234) *********************** 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 255 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: F 171 LYS cc_start: 0.7533 (mtpt) cc_final: 0.7299 (mtpt) REVERT: F 180 TYR cc_start: 0.8295 (p90) cc_final: 0.8030 (p90) REVERT: D 26 LYS cc_start: 0.6142 (pptt) cc_final: 0.5808 (pptt) REVERT: D 77 GLU cc_start: 0.6736 (tp30) cc_final: 0.6430 (tp30) REVERT: D 88 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 130 LEU cc_start: 0.7895 (mm) cc_final: 0.7343 (mm) REVERT: B 28 MET cc_start: 0.6742 (pmm) cc_final: 0.6540 (pmm) REVERT: B 158 GLU cc_start: 0.7904 (mp0) cc_final: 0.7410 (mp0) REVERT: H 28 ASP cc_start: 0.8078 (t0) cc_final: 0.7831 (t0) REVERT: H 40 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5875 (mtp) REVERT: H 198 GLU cc_start: 0.6919 (mp0) cc_final: 0.6286 (pm20) REVERT: H 283 GLN cc_start: 0.5725 (OUTLIER) cc_final: 0.5384 (pm20) outliers start: 39 outliers final: 21 residues processed: 242 average time/residue: 0.2557 time to fit residues: 89.3735 Evaluate side-chains 217 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 97 GLN C 71 ASN D 24 ASN B 206 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.160840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139378 restraints weight = 21502.728| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.31 r_work: 0.3696 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13340 Z= 0.176 Angle : 0.618 8.724 18234 Z= 0.332 Chirality : 0.045 0.402 2052 Planarity : 0.004 0.048 2120 Dihedral : 15.616 174.692 2470 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.75 % Favored : 92.90 % Rotamer: Outliers : 2.88 % Allowed : 16.76 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1422 helix: 0.70 (0.22), residues: 527 sheet: -1.18 (0.30), residues: 280 loop : -1.76 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 230 HIS 0.004 0.001 HIS F 62 PHE 0.033 0.002 PHE D 120 TYR 0.016 0.002 TYR C 87 ARG 0.005 0.001 ARG F 137 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 548) hydrogen bonds : angle 5.56274 ( 1572) covalent geometry : bond 0.00384 (13340) covalent geometry : angle 0.61770 (18234) *********************** 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 265 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: G 91 ILE cc_start: 0.6661 (mm) cc_final: 0.6417 (mm) REVERT: G 140 GLU cc_start: 0.7955 (pm20) cc_final: 0.7725 (pm20) REVERT: F 159 GLU cc_start: 0.5713 (tm-30) cc_final: 0.5347 (tm-30) REVERT: F 171 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7263 (mtpt) REVERT: F 180 TYR cc_start: 0.8304 (p90) cc_final: 0.8049 (p90) REVERT: C 118 LYS cc_start: 0.8085 (mppt) cc_final: 0.7188 (ttpp) REVERT: D 77 GLU cc_start: 0.6803 (tp30) cc_final: 0.6401 (tp30) REVERT: D 130 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7278 (mm) REVERT: B 100 HIS cc_start: 0.6755 (m-70) cc_final: 0.6357 (m170) REVERT: B 158 GLU cc_start: 0.7873 (mp0) cc_final: 0.7501 (mp0) REVERT: B 226 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5952 (tpp) REVERT: H 198 GLU cc_start: 0.6892 (mp0) cc_final: 0.6240 (pm20) REVERT: H 283 GLN cc_start: 0.5748 (OUTLIER) cc_final: 0.5439 (pm20) outliers start: 37 outliers final: 21 residues processed: 249 average time/residue: 0.2619 time to fit residues: 92.8190 Evaluate side-chains 229 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 226 MET 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 111 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 96 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.0670 chunk 126 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS E 125 ASN G 97 GLN C 71 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139554 restraints weight = 21473.292| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.34 r_work: 0.3689 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1817 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= 0.174 Angle : 0.612 9.059 18234 Z= 0.327 Chirality : 0.045 0.401 2052 Planarity : 0.004 0.048 2120 Dihedral : 15.514 174.552 2470 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.96 % Favored : 92.69 % Rotamer: Outliers : 3.82 % Allowed : 17.46 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1422 helix: 0.69 (0.22), residues: 540 sheet: -1.23 (0.30), residues: 275 loop : -1.72 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 301 HIS 0.004 0.001 HIS B 17 PHE 0.042 0.002 PHE D 120 TYR 0.015 0.001 TYR B 65 ARG 0.006 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 548) hydrogen bonds : angle 5.43676 ( 1572) covalent geometry : bond 0.00386 (13340) covalent geometry : angle 0.61189 (18234) *********************** 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 272 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: G 91 ILE cc_start: 0.6649 (mm) cc_final: 0.6430 (mm) REVERT: F 81 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7566 (ptp-170) REVERT: F 171 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7281 (mtpt) REVERT: F 180 TYR cc_start: 0.8341 (p90) cc_final: 0.7946 (p90) REVERT: C 118 LYS cc_start: 0.8073 (mppt) cc_final: 0.7153 (ttpp) REVERT: D 130 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7293 (mm) REVERT: B 158 GLU cc_start: 0.7963 (mp0) cc_final: 0.7551 (mp0) REVERT: B 226 MET cc_start: 0.6206 (OUTLIER) cc_final: 0.5966 (tpp) REVERT: H 40 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5660 (mtp) REVERT: H 198 GLU cc_start: 0.6956 (mp0) cc_final: 0.6251 (pm20) REVERT: H 283 GLN cc_start: 0.5736 (OUTLIER) cc_final: 0.5432 (pm20) outliers start: 49 outliers final: 28 residues processed: 255 average time/residue: 0.2555 time to fit residues: 93.3986 Evaluate side-chains 238 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 81 ARG 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 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 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 B residue 226 MET Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 0.8980 chunk 136 optimal weight: 0.0070 chunk 125 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 131 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN ** E 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN F 135 ASN C 71 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 206 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 = 0.4098 r_free = 0.4098 target = 0.163476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141831 restraints weight = 21553.607| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.33 r_work: 0.3723 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13340 Z= 0.139 Angle : 0.588 7.901 18234 Z= 0.316 Chirality : 0.044 0.384 2052 Planarity : 0.004 0.045 2120 Dihedral : 15.411 175.032 2468 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.12 % Favored : 93.53 % Rotamer: Outliers : 3.82 % Allowed : 18.47 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.22), residues: 1422 helix: 0.76 (0.22), residues: 542 sheet: -1.31 (0.30), residues: 290 loop : -1.70 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 230 HIS 0.004 0.001 HIS F 62 PHE 0.030 0.001 PHE D 120 TYR 0.016 0.001 TYR C 87 ARG 0.005 0.000 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 548) hydrogen bonds : angle 5.26809 ( 1572) covalent geometry : bond 0.00302 (13340) covalent geometry : angle 0.58764 (18234) *********************** 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 273 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 1.365 Fit side-chains REVERT: E 124 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: G 138 GLN cc_start: 0.7870 (tt0) cc_final: 0.7422 (mt0) REVERT: F 92 GLN cc_start: 0.7018 (pm20) cc_final: 0.6686 (pm20) REVERT: F 147 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: F 171 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7195 (mtpt) REVERT: F 180 TYR cc_start: 0.8221 (p90) cc_final: 0.8007 (p90) REVERT: C 22 LYS cc_start: 0.5008 (mmtt) cc_final: 0.4713 (mmtt) REVERT: C 63 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.7031 (t80) REVERT: C 118 LYS cc_start: 0.8021 (mppt) cc_final: 0.7110 (ttpp) REVERT: D 51 LEU cc_start: 0.7845 (mp) cc_final: 0.7624 (mt) REVERT: D 63 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: D 77 GLU cc_start: 0.6723 (tp30) cc_final: 0.6254 (tp30) REVERT: D 84 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6749 (mmtt) REVERT: D 130 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7273 (mm) REVERT: B 158 GLU cc_start: 0.7981 (mp0) cc_final: 0.7732 (mp0) REVERT: B 226 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.6136 (tpp) REVERT: H 198 GLU cc_start: 0.6941 (mp0) cc_final: 0.6308 (pm20) REVERT: H 283 GLN cc_start: 0.5572 (OUTLIER) cc_final: 0.5315 (pm20) outliers start: 49 outliers final: 25 residues processed: 258 average time/residue: 0.2858 time to fit residues: 105.3713 Evaluate side-chains 235 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain H residue 30 ILE 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 76 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 97 GLN F 97 GLN F 155 ASN C 41 ASN C 71 ASN B 106 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.157624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.135190 restraints weight = 21854.839| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.37 r_work: 0.3623 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13340 Z= 0.279 Angle : 0.706 8.871 18234 Z= 0.376 Chirality : 0.048 0.432 2052 Planarity : 0.005 0.114 2120 Dihedral : 15.584 172.667 2468 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.16 % Favored : 91.42 % Rotamer: Outliers : 4.21 % Allowed : 19.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.21), residues: 1422 helix: 0.64 (0.22), residues: 528 sheet: -1.38 (0.30), residues: 275 loop : -1.83 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 230 HIS 0.006 0.001 HIS B 17 PHE 0.028 0.002 PHE D 120 TYR 0.016 0.002 TYR H 155 ARG 0.005 0.001 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 548) hydrogen bonds : angle 5.62054 ( 1572) covalent geometry : bond 0.00626 (13340) covalent geometry : angle 0.70634 (18234) *********************** 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 269 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 215 time to evaluate : 1.385 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: G 87 GLU cc_start: 0.6032 (tt0) cc_final: 0.5749 (pt0) REVERT: F 147 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: F 171 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7281 (mtpt) REVERT: F 180 TYR cc_start: 0.8465 (p90) cc_final: 0.8081 (p90) REVERT: C 118 LYS cc_start: 0.8078 (mppt) cc_final: 0.7159 (ttpp) REVERT: D 63 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: D 72 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7156 (tm-30) REVERT: D 76 ASP cc_start: 0.6109 (m-30) cc_final: 0.5756 (m-30) REVERT: D 77 GLU cc_start: 0.6841 (tp30) cc_final: 0.6422 (tp30) REVERT: D 84 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6609 (mmtt) REVERT: D 130 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7232 (mm) REVERT: B 125 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7424 (p90) REVERT: B 158 GLU cc_start: 0.7995 (mp0) cc_final: 0.7698 (mp0) REVERT: B 246 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7773 (mmm-85) REVERT: H 40 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5619 (mtp) REVERT: H 198 GLU cc_start: 0.7082 (mp0) cc_final: 0.6396 (pm20) REVERT: H 224 LYS cc_start: 0.7763 (tttt) cc_final: 0.6840 (tmtt) REVERT: H 283 GLN cc_start: 0.5496 (OUTLIER) cc_final: 0.5236 (pm20) REVERT: H 290 THR cc_start: 0.7034 (m) cc_final: 0.6706 (p) outliers start: 54 outliers final: 31 residues processed: 250 average time/residue: 0.2496 time to fit residues: 89.9056 Evaluate side-chains 238 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain 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 139 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER 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 37 SER Chi-restraints excluded: chain B residue 125 TYR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 40 MET Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 307 VAL 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 1 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 97 GLN F 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 H 148 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139632 restraints weight = 21539.320| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.35 r_work: 0.3683 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13340 Z= 0.164 Angle : 0.628 9.603 18234 Z= 0.335 Chirality : 0.046 0.408 2052 Planarity : 0.004 0.076 2120 Dihedral : 15.535 174.766 2468 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.75 % Favored : 92.83 % Rotamer: Outliers : 3.35 % Allowed : 21.43 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1422 helix: 0.74 (0.22), residues: 541 sheet: -1.40 (0.30), residues: 275 loop : -1.76 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 230 HIS 0.004 0.001 HIS B 17 PHE 0.025 0.002 PHE D 120 TYR 0.020 0.001 TYR H 223 ARG 0.007 0.001 ARG H 52 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 548) hydrogen bonds : angle 5.37270 ( 1572) covalent geometry : bond 0.00368 (13340) covalent geometry : angle 0.62766 (18234) *********************** 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: 43 poor density : 214 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: E 124 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: G 138 GLN cc_start: 0.7919 (tt0) cc_final: 0.7490 (mt0) REVERT: F 147 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: F 171 LYS cc_start: 0.7512 (mtpt) cc_final: 0.7272 (mtpt) REVERT: F 180 TYR cc_start: 0.8347 (p90) cc_final: 0.7951 (p90) REVERT: C 63 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.7089 (t80) REVERT: C 118 LYS cc_start: 0.8023 (mppt) cc_final: 0.7123 (ttpp) REVERT: D 51 LEU cc_start: 0.7864 (mp) cc_final: 0.7654 (mt) REVERT: D 63 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.6965 (m-80) REVERT: D 72 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7178 (tm-30) REVERT: D 76 ASP cc_start: 0.5978 (m-30) cc_final: 0.5674 (m-30) REVERT: D 77 GLU cc_start: 0.6815 (tp30) cc_final: 0.6410 (tp30) REVERT: D 84 LYS cc_start: 0.7105 (mmtt) cc_final: 0.6628 (mmtt) REVERT: D 88 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 97 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7366 (mm-30) REVERT: D 130 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7161 (mm) REVERT: B 158 GLU cc_start: 0.7954 (mp0) cc_final: 0.7553 (mp0) REVERT: B 226 MET cc_start: 0.6251 (tpp) cc_final: 0.5887 (tpp) REVERT: B 246 ARG cc_start: 0.7865 (mmm160) cc_final: 0.7653 (mmm-85) REVERT: H 198 GLU cc_start: 0.7079 (mp0) cc_final: 0.6359 (pm20) REVERT: H 224 LYS cc_start: 0.7693 (tttt) cc_final: 0.6765 (tmtt) REVERT: H 283 GLN cc_start: 0.5409 (OUTLIER) cc_final: 0.5052 (mp10) outliers start: 43 outliers final: 29 residues processed: 242 average time/residue: 0.2798 time to fit residues: 96.0671 Evaluate side-chains 238 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 150 LYS Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 307 VAL Chi-restraints excluded: chain H residue 330 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS E 135 ASN G 97 GLN F 97 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133561 restraints weight = 21788.549| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.38 r_work: 0.3601 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 13340 Z= 0.320 Angle : 0.751 10.509 18234 Z= 0.398 Chirality : 0.050 0.444 2052 Planarity : 0.005 0.067 2120 Dihedral : 15.688 172.193 2468 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.51 % Favored : 91.14 % Rotamer: Outliers : 3.82 % Allowed : 21.82 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1422 helix: 0.54 (0.22), residues: 527 sheet: -1.51 (0.31), residues: 265 loop : -1.88 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 230 HIS 0.008 0.001 HIS B 17 PHE 0.026 0.002 PHE D 120 TYR 0.021 0.002 TYR H 223 ARG 0.006 0.001 ARG H 52 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 548) hydrogen bonds : angle 5.74086 ( 1572) covalent geometry : bond 0.00722 (13340) covalent geometry : angle 0.75072 (18234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: F 147 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: F 171 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7327 (mtpt) REVERT: F 180 TYR cc_start: 0.8536 (p90) cc_final: 0.8134 (p90) REVERT: C 118 LYS cc_start: 0.8107 (mppt) cc_final: 0.7208 (ttpp) REVERT: D 63 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: D 76 ASP cc_start: 0.6035 (m-30) cc_final: 0.5695 (m-30) REVERT: D 77 GLU cc_start: 0.6932 (tp30) cc_final: 0.6525 (tp30) REVERT: D 84 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6611 (mmtt) REVERT: D 88 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 97 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7497 (mm-30) REVERT: D 130 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7147 (mm) REVERT: B 125 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7379 (p90) REVERT: B 129 GLN cc_start: 0.7773 (mt0) cc_final: 0.7518 (mt0) REVERT: B 158 GLU cc_start: 0.8086 (mp0) cc_final: 0.7728 (mp0) REVERT: B 246 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7848 (mmm-85) REVERT: H 224 LYS cc_start: 0.7782 (tttt) cc_final: 0.6801 (tmtt) REVERT: H 283 GLN cc_start: 0.5501 (OUTLIER) cc_final: 0.5118 (mp10) REVERT: H 290 THR cc_start: 0.7055 (m) cc_final: 0.6709 (p) outliers start: 49 outliers final: 33 residues processed: 232 average time/residue: 0.2624 time to fit residues: 87.7027 Evaluate side-chains 233 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain F residue 3 SER Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 125 TYR 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 38 VAL Chi-restraints excluded: chain H residue 149 GLU 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 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 69 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 110 HIS E 135 ASN G 97 GLN F 97 GLN C 41 ASN B 100 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN H 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.161875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139990 restraints weight = 21544.960| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.35 r_work: 0.3695 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13340 Z= 0.155 Angle : 0.640 10.966 18234 Z= 0.342 Chirality : 0.046 0.406 2052 Planarity : 0.004 0.051 2120 Dihedral : 15.607 175.103 2468 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.25 % Rotamer: Outliers : 2.34 % Allowed : 23.77 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1422 helix: 0.76 (0.23), residues: 535 sheet: -1.45 (0.30), residues: 275 loop : -1.78 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 230 HIS 0.003 0.001 HIS F 62 PHE 0.029 0.002 PHE C 63 TYR 0.024 0.002 TYR C 87 ARG 0.008 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 548) hydrogen bonds : angle 5.40861 ( 1572) covalent geometry : bond 0.00344 (13340) covalent geometry : angle 0.63980 (18234) *********************** 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 245 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 138 GLN cc_start: 0.7937 (tt0) cc_final: 0.7514 (mt0) REVERT: F 42 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8536 (ttpt) REVERT: F 147 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: F 171 LYS cc_start: 0.7503 (mtpt) cc_final: 0.7278 (mtpt) REVERT: F 180 TYR cc_start: 0.8382 (p90) cc_final: 0.7996 (p90) REVERT: C 118 LYS cc_start: 0.8030 (mppt) cc_final: 0.7149 (ttpp) REVERT: D 51 LEU cc_start: 0.7924 (mp) cc_final: 0.7706 (mt) REVERT: D 63 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: D 72 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7166 (tm-30) REVERT: D 76 ASP cc_start: 0.5916 (m-30) cc_final: 0.5714 (m-30) REVERT: D 77 GLU cc_start: 0.6862 (tp30) cc_final: 0.6452 (tp30) REVERT: D 84 LYS cc_start: 0.7066 (mmtt) cc_final: 0.6539 (mmtt) REVERT: D 88 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7610 (mm-30) REVERT: D 130 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7120 (mm) REVERT: B 129 GLN cc_start: 0.7680 (mt0) cc_final: 0.7353 (mt0) REVERT: B 158 GLU cc_start: 0.8023 (mp0) cc_final: 0.7585 (mp0) REVERT: H 119 MET cc_start: 0.8074 (ppp) cc_final: 0.7736 (ptm) REVERT: H 198 GLU cc_start: 0.7068 (mp0) cc_final: 0.6353 (pm20) REVERT: H 224 LYS cc_start: 0.7585 (tttt) cc_final: 0.6639 (tmtt) REVERT: H 283 GLN cc_start: 0.5454 (OUTLIER) cc_final: 0.5049 (mp10) outliers start: 30 outliers final: 24 residues processed: 235 average time/residue: 0.2614 time to fit residues: 87.5925 Evaluate side-chains 231 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER 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 220 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS F 97 GLN F 155 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135070 restraints weight = 21738.961| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.36 r_work: 0.3623 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13340 Z= 0.273 Angle : 0.741 13.634 18234 Z= 0.388 Chirality : 0.049 0.434 2052 Planarity : 0.005 0.059 2120 Dihedral : 15.678 172.735 2468 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.51 % Favored : 91.14 % Rotamer: Outliers : 2.96 % Allowed : 22.84 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.21), residues: 1422 helix: 0.64 (0.22), residues: 528 sheet: -1.56 (0.31), residues: 265 loop : -1.81 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 230 HIS 0.007 0.001 HIS B 17 PHE 0.029 0.002 PHE C 63 TYR 0.025 0.002 TYR C 87 ARG 0.009 0.001 ARG H 64 Details of bonding type rmsd hydrogen bonds : bond 0.04915 ( 548) hydrogen bonds : angle 5.64730 ( 1572) covalent geometry : bond 0.00619 (13340) covalent geometry : angle 0.74051 (18234) ********************** 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 232 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: F 42 LYS cc_start: 0.8760 (ttpp) cc_final: 0.8485 (ttpt) REVERT: F 147 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: F 171 LYS cc_start: 0.7588 (mtpt) cc_final: 0.7320 (mtpt) REVERT: F 180 TYR cc_start: 0.8513 (p90) cc_final: 0.8102 (p90) REVERT: C 118 LYS cc_start: 0.8078 (mppt) cc_final: 0.7170 (ttpp) REVERT: D 63 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: D 72 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7294 (tm-30) REVERT: D 76 ASP cc_start: 0.5932 (m-30) cc_final: 0.5711 (m-30) REVERT: D 77 GLU cc_start: 0.6875 (tp30) cc_final: 0.6465 (tp30) REVERT: D 84 LYS cc_start: 0.7160 (mmtt) cc_final: 0.6609 (mmtt) REVERT: D 88 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 130 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7110 (mm) REVERT: B 129 GLN cc_start: 0.7733 (mt0) cc_final: 0.7465 (mt0) REVERT: B 138 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6451 (tt0) REVERT: B 158 GLU cc_start: 0.8058 (mp0) cc_final: 0.7586 (mp0) REVERT: B 226 MET cc_start: 0.5929 (tpp) cc_final: 0.5219 (mpp) REVERT: H 224 LYS cc_start: 0.7666 (tttt) cc_final: 0.6718 (tmtt) REVERT: H 283 GLN cc_start: 0.5394 (OUTLIER) cc_final: 0.4996 (mp10) REVERT: H 290 THR cc_start: 0.7046 (m) cc_final: 0.6728 (p) outliers start: 38 outliers final: 30 residues processed: 223 average time/residue: 0.2682 time to fit residues: 84.1986 Evaluate side-chains 224 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 103 PHE Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 174 HIS Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 94 SER 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 59 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain H residue 38 VAL 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 10 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 110 HIS G 97 GLN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134982 restraints weight = 21650.706| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.36 r_work: 0.3629 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 13340 Z= 0.248 Angle : 0.968 59.200 18234 Z= 0.537 Chirality : 0.048 0.424 2052 Planarity : 0.006 0.135 2120 Dihedral : 15.685 172.892 2468 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.51 % Favored : 91.14 % Rotamer: Outliers : 2.57 % Allowed : 23.46 % Favored : 73.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1422 helix: 0.64 (0.22), residues: 528 sheet: -1.59 (0.31), residues: 265 loop : -1.82 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 230 HIS 0.007 0.001 HIS B 17 PHE 0.027 0.002 PHE C 63 TYR 0.020 0.002 TYR C 87 ARG 0.010 0.001 ARG B 295 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 548) hydrogen bonds : angle 5.64004 ( 1572) covalent geometry : bond 0.00564 (13340) covalent geometry : angle 0.96801 (18234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5856.73 seconds wall clock time: 103 minutes 6.84 seconds (6186.84 seconds total)