Starting phenix.real_space_refine on Thu Feb 5 14:42:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyv_15027/02_2026/7zyv_15027_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyv_15027/02_2026/7zyv_15027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zyv_15027/02_2026/7zyv_15027_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyv_15027/02_2026/7zyv_15027_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zyv_15027/02_2026/7zyv_15027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyv_15027/02_2026/7zyv_15027.map" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 Mg 2 5.21 5 S 72 5.16 5 C 11008 2.51 5 N 2500 2.21 5 O 2858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16452 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1225 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2158 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 23, 'TRANS': 254} Chain breaks: 1 Chain: "D" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1259 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2167 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1254 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain breaks: 1 Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "O" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 317 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 262 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'UMQ': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'HEC': 1, 'PL9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'BCR': 1, 'UMQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5784 SG CYS D 107 42.317 69.391 44.000 1.00 96.15 S ATOM 5920 SG CYS D 125 40.722 65.931 43.166 1.00 95.70 S ATOM 13133 SG CYS L 107 93.565 26.930 43.993 1.00 96.40 S ATOM 13269 SG CYS L 125 95.166 30.393 43.162 1.00 96.16 S Time building chain proxies: 3.19, per 1000 atoms: 0.19 Number of scatterers: 16452 At special positions: 0 Unit cell: (136.74, 97.18, 122.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 72 16.00 Mg 2 11.99 O 2858 8.00 N 2500 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.03 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 450.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 202 " - pdb=" SG CYS D 125 " pdb="FE2 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 202 " - pdb=" ND1 HIS D 109 " pdb=" FES L 402 " pdb="FE1 FES L 402 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 402 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 402 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 402 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 14 sheets defined 52.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.811A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.619A pdb=" N ALA A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.671A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 137 removed outlier: 3.769A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.583A pdb=" N ALA A 157 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.654A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.729A pdb=" N LEU A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 39 through 58 removed outlier: 3.548A pdb=" N VAL B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 93 through 110 removed outlier: 4.031A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.753A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 147 Processing helix chain 'B' and resid 148 through 149 No H-bonds generated for 'chain 'B' and resid 148 through 149' Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.702A pdb=" N ILE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.774A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.557A pdb=" N LYS C 138 " --> pdb=" O PRO C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.626A pdb=" N ILE C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 41 removed outlier: 3.650A pdb=" N SER D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix removed outlier: 4.134A pdb=" N PHE D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.985A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS D 72 " --> pdb=" O TRP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 28 Processing helix chain 'F' and resid 2 through 35 removed outlier: 3.836A pdb=" N THR F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.876A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.675A pdb=" N LEU H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.811A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 removed outlier: 3.619A pdb=" N ALA I 18 " --> pdb=" O ILE I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 34 Processing helix chain 'I' and resid 35 through 55 Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 78 through 107 removed outlier: 3.671A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.769A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 Processing helix chain 'I' and resid 153 through 158 removed outlier: 3.582A pdb=" N ALA I 157 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.653A pdb=" N LEU I 165 " --> pdb=" O ILE I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 removed outlier: 3.730A pdb=" N LEU I 193 " --> pdb=" O PHE I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 19 Processing helix chain 'J' and resid 39 through 58 removed outlier: 3.550A pdb=" N VAL J 43 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'J' and resid 93 through 110 removed outlier: 4.031A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.753A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.702A pdb=" N ILE K 89 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.774A pdb=" N GLY K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.557A pdb=" N LYS K 138 " --> pdb=" O PRO K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.625A pdb=" N ILE K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 removed outlier: 3.556A pdb=" N GLU L 16 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix removed outlier: 3.678A pdb=" N LEU L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Proline residue: L 36 - end of helix Processing helix chain 'L' and resid 64 through 72 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 28 Processing helix chain 'N' and resid 2 through 34 removed outlier: 3.872A pdb=" N THR N 17 " --> pdb=" O MET N 13 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 32 removed outlier: 3.876A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 26 removed outlier: 3.684A pdb=" N LEU P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 43 removed outlier: 3.550A pdb=" N LYS R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 43 removed outlier: 3.550A pdb=" N LYS Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.747A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.320A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE C 112 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 103 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'C' and resid 204 through 207 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.896A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 103 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.348A pdb=" N GLN D 131 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.747A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.319A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE K 112 " --> pdb=" O TYR K 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN K 103 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'K' and resid 203 through 207 Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.881A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 103 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.347A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2277 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 6621 1.41 - 1.61: 10127 1.61 - 1.81: 110 1.81 - 2.01: 4 2.01 - 2.20: 48 Bond restraints: 16910 Sorted by residual: bond pdb=" C1 SQD L 401 " pdb=" O5 SQD L 401 " ideal model delta sigma weight residual 1.500 1.397 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 SQD D 201 " pdb=" O5 SQD D 201 " ideal model delta sigma weight residual 1.500 1.398 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C5' UMQ B 403 " pdb=" O5' UMQ B 403 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C5' UMQ J 404 " pdb=" O5' UMQ J 404 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C5 SQD L 401 " pdb=" O5 SQD L 401 " ideal model delta sigma weight residual 1.483 1.402 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 16905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 22577 2.11 - 4.22: 437 4.22 - 6.33: 66 6.33 - 8.44: 13 8.44 - 10.55: 6 Bond angle restraints: 23099 Sorted by residual: angle pdb=" N ARG E 29 " pdb=" CA ARG E 29 " pdb=" C ARG E 29 " ideal model delta sigma weight residual 112.86 117.39 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" CG LYS C 222 " pdb=" CD LYS C 222 " pdb=" CE LYS C 222 " ideal model delta sigma weight residual 111.30 119.56 -8.26 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CG LYS K 222 " pdb=" CD LYS K 222 " pdb=" CE LYS K 222 " ideal model delta sigma weight residual 111.30 119.55 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" N LYS B 119 " pdb=" CA LYS B 119 " pdb=" C LYS B 119 " ideal model delta sigma weight residual 112.59 116.63 -4.04 1.22e+00 6.72e-01 1.10e+01 angle pdb=" CD LYS C 222 " pdb=" CE LYS C 222 " pdb=" NZ LYS C 222 " ideal model delta sigma weight residual 111.90 122.45 -10.55 3.20e+00 9.77e-02 1.09e+01 ... (remaining 23094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.05: 9221 27.05 - 54.11: 743 54.11 - 81.16: 112 81.16 - 108.21: 54 108.21 - 135.27: 13 Dihedral angle restraints: 10143 sinusoidal: 4595 harmonic: 5548 Sorted by residual: dihedral pdb=" CA LYS D 96 " pdb=" C LYS D 96 " pdb=" N THR D 97 " pdb=" CA THR D 97 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" O2 UMQ B 404 " pdb=" C1 UMQ B 404 " pdb=" C2 UMQ B 404 " pdb=" O5 UMQ B 404 " ideal model delta sinusoidal sigma weight residual 177.88 -46.85 -135.27 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" O1 UMQ B 404 " pdb=" C1 UMQ B 404 " pdb=" C2 UMQ B 404 " pdb=" O2 UMQ B 404 " ideal model delta sinusoidal sigma weight residual 59.79 -74.43 134.22 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 10140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2531 0.121 - 0.243: 34 0.243 - 0.364: 4 0.364 - 0.486: 1 0.486 - 0.607: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" C1 UMQ B 403 " pdb=" C2 UMQ B 403 " pdb=" O1 UMQ B 403 " pdb=" O5 UMQ B 403 " both_signs ideal model delta sigma weight residual False -2.24 -1.64 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" C1 UMQ J 404 " pdb=" C2 UMQ J 404 " pdb=" O1 UMQ J 404 " pdb=" O5 UMQ J 404 " both_signs ideal model delta sigma weight residual False -2.24 -1.64 -0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" C1 SQD D 201 " pdb=" C2 SQD D 201 " pdb=" O5 SQD D 201 " pdb=" O6 SQD D 201 " both_signs ideal model delta sigma weight residual False -2.39 -2.02 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2569 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 SQD L 401 " 0.101 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C8 SQD L 401 " -0.030 2.00e-02 2.50e+03 pdb=" O47 SQD L 401 " -0.033 2.00e-02 2.50e+03 pdb=" O49 SQD L 401 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR F 101 " 0.038 2.00e-02 2.50e+03 3.89e-02 1.89e+01 pdb=" C21 BCR F 101 " -0.066 2.00e-02 2.50e+03 pdb=" C22 BCR F 101 " 0.033 2.00e-02 2.50e+03 pdb=" C23 BCR F 101 " 0.015 2.00e-02 2.50e+03 pdb=" C37 BCR F 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.031 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C21 BCR P 101 " -0.060 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " 0.045 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.006 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.022 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 65 2.52 - 3.12: 11705 3.12 - 3.71: 22971 3.71 - 4.31: 33120 4.31 - 4.90: 57151 Nonbonded interactions: 125012 Sorted by model distance: nonbonded pdb=" O2 UMQ J 404 " pdb=" O3' UMQ J 404 " model vdw 1.927 3.040 nonbonded pdb=" O2 UMQ B 403 " pdb=" O3' UMQ B 403 " model vdw 1.928 3.040 nonbonded pdb=" O2 UMQ A 305 " pdb=" O3' UMQ A 305 " model vdw 1.985 3.040 nonbonded pdb=" O GLY K 177 " pdb=" OG SER K 220 " model vdw 2.003 3.040 nonbonded pdb=" O GLY C 177 " pdb=" OG SER C 220 " model vdw 2.004 3.040 ... (remaining 125007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 306) selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'J' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 401 through 404)) } ncs_group { reference = chain 'C' selection = (chain 'K' and (resid 1 through 195 or resid 203 through 301)) } ncs_group { reference = (chain 'D' and (resid 8 through 178 or resid 201 through 202)) selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = chain 'N' } ncs_group { reference = (chain 'G' and resid 1 through 33) selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 1 through 29) selection = (chain 'P' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)))) } ncs_group { reference = chain 'Q' selection = chain 'R' } 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: 3.030 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.950 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 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 : 0.013 0.523 16931 Z= 0.396 Angle : 0.705 10.545 23109 Z= 0.326 Chirality : 0.051 0.607 2572 Planarity : 0.005 0.058 2761 Dihedral : 20.577 135.267 6577 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.20 % Allowed : 19.30 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1902 helix: 2.34 (0.17), residues: 946 sheet: 0.11 (0.37), residues: 188 loop : -1.45 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 137 TYR 0.011 0.001 TYR K 190 PHE 0.011 0.001 PHE I 131 TRP 0.013 0.001 TRP I 146 HIS 0.003 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00738 (16910) covalent geometry : angle 0.70128 (23099) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.75018 ( 4) hydrogen bonds : bond 0.15044 ( 800) hydrogen bonds : angle 5.24118 ( 2277) metal coordination : bond 0.34279 ( 8) metal coordination : angle 4.82504 ( 6) Misc. bond : bond 0.31100 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.430 Fit side-chains REVERT: C 184 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7246 (tmm160) REVERT: D 137 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8089 (ttp80) REVERT: J 152 ASP cc_start: 0.8793 (p0) cc_final: 0.8571 (p0) outliers start: 36 outliers final: 26 residues processed: 215 average time/residue: 0.6702 time to fit residues: 156.3408 Evaluate side-chains 192 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain K residue 124 SER Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.055621 restraints weight = 25636.967| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.99 r_work: 0.2546 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 16931 Z= 0.163 Angle : 0.719 11.668 23109 Z= 0.330 Chirality : 0.047 0.189 2572 Planarity : 0.005 0.047 2761 Dihedral : 17.327 110.907 3117 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.30 % Allowed : 16.98 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.20), residues: 1902 helix: 2.49 (0.17), residues: 960 sheet: -0.00 (0.35), residues: 198 loop : -1.31 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 184 TYR 0.013 0.001 TYR K 190 PHE 0.019 0.001 PHE A 52 TRP 0.012 0.001 TRP A 146 HIS 0.004 0.001 HIS L 72 Details of bonding type rmsd covalent geometry : bond 0.00366 (16910) covalent geometry : angle 0.71633 (23099) SS BOND : bond 0.00445 ( 2) SS BOND : angle 1.47900 ( 4) hydrogen bonds : bond 0.08463 ( 800) hydrogen bonds : angle 3.97839 ( 2277) metal coordination : bond 0.01210 ( 8) metal coordination : angle 3.77623 ( 6) Misc. bond : bond 0.06079 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: D 140 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8331 (tmm-80) REVERT: D 166 GLU cc_start: 0.7816 (mp0) cc_final: 0.7564 (OUTLIER) REVERT: F 36 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: K 184 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7719 (tpt90) REVERT: L 54 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8339 (mt) REVERT: L 140 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8304 (tmm-80) outliers start: 54 outliers final: 23 residues processed: 214 average time/residue: 0.7212 time to fit residues: 167.1513 Evaluate side-chains 204 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.056589 restraints weight = 25766.983| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.00 r_work: 0.2569 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 16931 Z= 0.149 Angle : 0.662 10.840 23109 Z= 0.305 Chirality : 0.045 0.187 2572 Planarity : 0.005 0.051 2761 Dihedral : 15.312 93.197 3098 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.99 % Allowed : 17.65 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1902 helix: 2.55 (0.17), residues: 967 sheet: 0.10 (0.35), residues: 206 loop : -1.30 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 137 TYR 0.010 0.001 TYR C 190 PHE 0.015 0.001 PHE J 160 TRP 0.011 0.001 TRP A 146 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00332 (16910) covalent geometry : angle 0.66005 (23099) SS BOND : bond 0.00399 ( 2) SS BOND : angle 1.21595 ( 4) hydrogen bonds : bond 0.07930 ( 800) hydrogen bonds : angle 3.82870 ( 2277) metal coordination : bond 0.00856 ( 8) metal coordination : angle 3.18370 ( 6) Misc. bond : bond 0.05801 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8753 (m-80) REVERT: B 119 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8545 (pptt) REVERT: C 54 ASP cc_start: 0.8518 (t0) cc_final: 0.8302 (t0) REVERT: C 154 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8074 (pmm150) REVERT: D 168 ASP cc_start: 0.8317 (t0) cc_final: 0.8069 (t0) REVERT: F 36 GLU cc_start: 0.8751 (pm20) cc_final: 0.8314 (pm20) REVERT: G 3 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8383 (mm-30) REVERT: I 131 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: J 152 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8654 (p0) REVERT: K 154 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8081 (pmm150) REVERT: O 3 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8400 (mm-30) outliers start: 49 outliers final: 22 residues processed: 210 average time/residue: 0.6980 time to fit residues: 159.3206 Evaluate side-chains 206 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 117 optimal weight: 0.0170 chunk 66 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.094893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058943 restraints weight = 25928.602| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.01 r_work: 0.2620 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 16931 Z= 0.130 Angle : 0.622 10.011 23109 Z= 0.286 Chirality : 0.045 0.284 2572 Planarity : 0.005 0.050 2761 Dihedral : 14.170 89.331 3098 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.38 % Allowed : 18.81 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1902 helix: 2.77 (0.17), residues: 957 sheet: 0.26 (0.35), residues: 206 loop : -1.22 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 137 TYR 0.009 0.001 TYR K 190 PHE 0.014 0.001 PHE A 52 TRP 0.010 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00282 (16910) covalent geometry : angle 0.61919 (23099) SS BOND : bond 0.00284 ( 2) SS BOND : angle 0.94563 ( 4) hydrogen bonds : bond 0.06693 ( 800) hydrogen bonds : angle 3.65216 ( 2277) metal coordination : bond 0.00521 ( 8) metal coordination : angle 3.40664 ( 6) Misc. bond : bond 0.05445 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8502 (t0) cc_final: 0.8247 (t0) REVERT: C 283 MET cc_start: 0.8089 (tpp) cc_final: 0.7875 (tpt) REVERT: D 67 GLU cc_start: 0.9292 (mp0) cc_final: 0.8906 (pm20) REVERT: D 137 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7500 (mtm-85) REVERT: F 36 GLU cc_start: 0.8717 (pm20) cc_final: 0.8273 (pm20) REVERT: K 54 ASP cc_start: 0.8536 (t0) cc_final: 0.8222 (t0) REVERT: L 32 TYR cc_start: 0.8406 (m-80) cc_final: 0.7786 (t80) outliers start: 39 outliers final: 20 residues processed: 211 average time/residue: 0.7245 time to fit residues: 166.2992 Evaluate side-chains 197 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 180 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 131 optimal weight: 0.4980 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.057661 restraints weight = 25965.882| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.00 r_work: 0.2592 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 16931 Z= 0.140 Angle : 0.633 10.218 23109 Z= 0.292 Chirality : 0.045 0.342 2572 Planarity : 0.005 0.050 2761 Dihedral : 13.430 89.230 3091 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.26 % Allowed : 18.81 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 1902 helix: 2.75 (0.17), residues: 957 sheet: 0.34 (0.34), residues: 206 loop : -1.19 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 137 TYR 0.008 0.001 TYR K 190 PHE 0.013 0.001 PHE A 52 TRP 0.010 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00309 (16910) covalent geometry : angle 0.63176 (23099) SS BOND : bond 0.00381 ( 2) SS BOND : angle 1.16403 ( 4) hydrogen bonds : bond 0.07369 ( 800) hydrogen bonds : angle 3.67883 ( 2277) metal coordination : bond 0.00634 ( 8) metal coordination : angle 2.82787 ( 6) Misc. bond : bond 0.05577 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8473 (t0) cc_final: 0.8187 (t0) REVERT: C 283 MET cc_start: 0.7968 (tpp) cc_final: 0.7745 (tpt) REVERT: D 67 GLU cc_start: 0.9294 (mp0) cc_final: 0.8933 (pm20) REVERT: D 137 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7569 (mtm-85) REVERT: D 173 GLU cc_start: 0.8916 (pt0) cc_final: 0.8419 (pm20) REVERT: G 3 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8333 (mm-30) REVERT: K 54 ASP cc_start: 0.8554 (t0) cc_final: 0.8229 (t0) REVERT: K 184 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7871 (tmm-80) REVERT: K 222 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8511 (ptmm) REVERT: L 32 TYR cc_start: 0.8387 (m-80) cc_final: 0.7800 (t80) REVERT: O 3 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8359 (mm-30) REVERT: O 31 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7662 (ttp-170) outliers start: 37 outliers final: 22 residues processed: 204 average time/residue: 0.7635 time to fit residues: 169.0593 Evaluate side-chains 203 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 127 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.092236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.055609 restraints weight = 25852.216| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.00 r_work: 0.2543 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 16931 Z= 0.165 Angle : 0.668 12.008 23109 Z= 0.310 Chirality : 0.046 0.285 2572 Planarity : 0.005 0.050 2761 Dihedral : 13.290 89.030 3090 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.38 % Allowed : 18.63 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1902 helix: 2.59 (0.17), residues: 963 sheet: 0.21 (0.33), residues: 216 loop : -1.16 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 29 TYR 0.008 0.001 TYR K 190 PHE 0.014 0.001 PHE I 52 TRP 0.011 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00385 (16910) covalent geometry : angle 0.66625 (23099) SS BOND : bond 0.00501 ( 2) SS BOND : angle 1.47565 ( 4) hydrogen bonds : bond 0.08600 ( 800) hydrogen bonds : angle 3.79778 ( 2277) metal coordination : bond 0.00697 ( 8) metal coordination : angle 2.49344 ( 6) Misc. bond : bond 0.06536 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8505 (t0) cc_final: 0.8210 (t0) REVERT: D 67 GLU cc_start: 0.9326 (mp0) cc_final: 0.8980 (pm20) REVERT: D 137 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7595 (mtm-85) REVERT: D 173 GLU cc_start: 0.8915 (pt0) cc_final: 0.8429 (pm20) REVERT: G 3 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8322 (mm-30) REVERT: K 54 ASP cc_start: 0.8582 (t0) cc_final: 0.8266 (t0) REVERT: K 194 ILE cc_start: 0.9313 (pp) cc_final: 0.8661 (mp) REVERT: L 32 TYR cc_start: 0.8426 (m-80) cc_final: 0.7796 (t80) REVERT: O 3 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8361 (mm-30) REVERT: O 31 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7845 (ttp-170) outliers start: 39 outliers final: 23 residues processed: 204 average time/residue: 0.8557 time to fit residues: 188.9421 Evaluate side-chains 206 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.0050 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 0.0470 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 20.0000 overall best weight: 0.9894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.057601 restraints weight = 25819.705| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.01 r_work: 0.2590 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 16931 Z= 0.141 Angle : 0.632 10.213 23109 Z= 0.296 Chirality : 0.045 0.244 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.953 89.914 3090 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 19.12 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1902 helix: 2.72 (0.17), residues: 957 sheet: 0.22 (0.33), residues: 216 loop : -1.18 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 29 TYR 0.008 0.001 TYR K 53 PHE 0.014 0.001 PHE A 52 TRP 0.011 0.001 TRP A 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00310 (16910) covalent geometry : angle 0.63069 (23099) SS BOND : bond 0.00354 ( 2) SS BOND : angle 1.08944 ( 4) hydrogen bonds : bond 0.07405 ( 800) hydrogen bonds : angle 3.68968 ( 2277) metal coordination : bond 0.00541 ( 8) metal coordination : angle 2.86169 ( 6) Misc. bond : bond 0.06173 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8492 (t0) cc_final: 0.8234 (t0) REVERT: D 67 GLU cc_start: 0.9334 (mp0) cc_final: 0.8973 (pm20) REVERT: D 137 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7625 (mtm-85) REVERT: D 173 GLU cc_start: 0.8922 (pt0) cc_final: 0.8432 (pm20) REVERT: G 3 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8324 (mm-30) REVERT: K 54 ASP cc_start: 0.8560 (t0) cc_final: 0.8265 (t0) REVERT: L 32 TYR cc_start: 0.8410 (m-80) cc_final: 0.7781 (t80) REVERT: O 3 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: O 31 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7663 (ttp-170) outliers start: 35 outliers final: 23 residues processed: 195 average time/residue: 0.8805 time to fit residues: 185.3282 Evaluate side-chains 192 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 180 optimal weight: 0.0670 chunk 55 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.056170 restraints weight = 25664.490| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.00 r_work: 0.2555 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 16931 Z= 0.156 Angle : 0.653 11.438 23109 Z= 0.305 Chirality : 0.045 0.195 2572 Planarity : 0.005 0.049 2761 Dihedral : 12.872 89.468 3090 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 18.63 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1902 helix: 2.59 (0.17), residues: 961 sheet: 0.28 (0.33), residues: 216 loop : -1.17 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 29 TYR 0.008 0.001 TYR K 190 PHE 0.014 0.001 PHE I 52 TRP 0.010 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00356 (16910) covalent geometry : angle 0.65191 (23099) SS BOND : bond 0.00451 ( 2) SS BOND : angle 1.36617 ( 4) hydrogen bonds : bond 0.08309 ( 800) hydrogen bonds : angle 3.76331 ( 2277) metal coordination : bond 0.00659 ( 8) metal coordination : angle 2.47435 ( 6) Misc. bond : bond 0.06484 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: D 67 GLU cc_start: 0.9352 (mp0) cc_final: 0.8996 (pm20) REVERT: D 137 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7644 (mtm-85) REVERT: D 173 GLU cc_start: 0.8923 (pt0) cc_final: 0.8428 (pm20) REVERT: G 3 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8323 (mm-30) REVERT: K 194 ILE cc_start: 0.9265 (pp) cc_final: 0.8971 (mm) REVERT: O 3 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8385 (mm-30) REVERT: O 31 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7809 (ttp-170) outliers start: 35 outliers final: 24 residues processed: 192 average time/residue: 0.9269 time to fit residues: 191.4501 Evaluate side-chains 199 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 113 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 69 optimal weight: 0.0980 chunk 57 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.059549 restraints weight = 26007.619| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.00 r_work: 0.2633 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 16931 Z= 0.128 Angle : 0.601 9.719 23109 Z= 0.282 Chirality : 0.043 0.187 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.379 89.935 3090 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 19.12 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1902 helix: 2.78 (0.17), residues: 954 sheet: 0.30 (0.32), residues: 216 loop : -1.12 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 30 TYR 0.009 0.001 TYR C 53 PHE 0.012 0.001 PHE A 131 TRP 0.010 0.001 TRP A 146 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00276 (16910) covalent geometry : angle 0.59928 (23099) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.89431 ( 4) hydrogen bonds : bond 0.06545 ( 800) hydrogen bonds : angle 3.59558 ( 2277) metal coordination : bond 0.00409 ( 8) metal coordination : angle 3.09513 ( 6) Misc. bond : bond 0.05802 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: D 67 GLU cc_start: 0.9363 (mp0) cc_final: 0.9010 (pm20) REVERT: D 137 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7608 (mtm-85) REVERT: D 173 GLU cc_start: 0.8941 (pt0) cc_final: 0.8438 (pm20) REVERT: K 194 ILE cc_start: 0.9262 (pp) cc_final: 0.8942 (mm) REVERT: L 32 TYR cc_start: 0.8377 (m-80) cc_final: 0.7778 (t80) REVERT: L 140 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7818 (tpt-90) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.8990 time to fit residues: 190.2172 Evaluate side-chains 196 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 141 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 106 optimal weight: 0.0050 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.055934 restraints weight = 25538.537| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.00 r_work: 0.2540 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 16931 Z= 0.161 Angle : 0.662 11.681 23109 Z= 0.310 Chirality : 0.045 0.189 2572 Planarity : 0.005 0.049 2761 Dihedral : 12.511 89.405 3088 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.47 % Allowed : 19.61 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.19), residues: 1902 helix: 2.60 (0.17), residues: 958 sheet: 0.30 (0.32), residues: 216 loop : -1.14 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 29 TYR 0.008 0.001 TYR I 105 PHE 0.014 0.001 PHE I 52 TRP 0.010 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00376 (16910) covalent geometry : angle 0.66041 (23099) SS BOND : bond 0.00488 ( 2) SS BOND : angle 1.41722 ( 4) hydrogen bonds : bond 0.08370 ( 800) hydrogen bonds : angle 3.75523 ( 2277) metal coordination : bond 0.00660 ( 8) metal coordination : angle 2.41748 ( 6) Misc. bond : bond 0.06423 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.636 Fit side-chains REVERT: D 67 GLU cc_start: 0.9347 (mp0) cc_final: 0.9005 (pm20) REVERT: D 137 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7632 (mtm-85) REVERT: D 173 GLU cc_start: 0.8929 (pt0) cc_final: 0.8426 (pm20) REVERT: G 31 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7704 (ttp-170) REVERT: K 194 ILE cc_start: 0.9297 (pp) cc_final: 0.8973 (mm) REVERT: L 140 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7884 (tpt-90) REVERT: O 31 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7741 (ttp-170) outliers start: 24 outliers final: 16 residues processed: 186 average time/residue: 0.9307 time to fit residues: 186.2538 Evaluate side-chains 191 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.058446 restraints weight = 25713.227| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 1.99 r_work: 0.2598 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 16931 Z= 0.134 Angle : 0.631 10.334 23109 Z= 0.297 Chirality : 0.043 0.188 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.230 89.764 3088 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.98 % Allowed : 20.16 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1902 helix: 2.73 (0.17), residues: 954 sheet: 0.30 (0.32), residues: 216 loop : -1.10 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 29 TYR 0.008 0.001 TYR K 190 PHE 0.013 0.001 PHE A 52 TRP 0.011 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00292 (16910) covalent geometry : angle 0.62926 (23099) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.94963 ( 4) hydrogen bonds : bond 0.06944 ( 800) hydrogen bonds : angle 3.65588 ( 2277) metal coordination : bond 0.00460 ( 8) metal coordination : angle 2.94729 ( 6) Misc. bond : bond 0.05985 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8987.83 seconds wall clock time: 153 minutes 1.93 seconds (9181.93 seconds total)