Starting phenix.real_space_refine on Mon Jun 16 06:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zyv_15027/06_2025/7zyv_15027_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zyv_15027/06_2025/7zyv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zyv_15027/06_2025/7zyv_15027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zyv_15027/06_2025/7zyv_15027.map" model { file = "/net/cci-nas-00/data/ceres_data/7zyv_15027/06_2025/7zyv_15027_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zyv_15027/06_2025/7zyv_15027_trim.cif" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.95, per 1000 atoms: 0.67 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: 5.03 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.75 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: 4.43 Time building geometry restraints manager: 5.61 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 215 or resid 301 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 285 or resid 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: 2.130 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 42.130 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.170 ------------------------------------------------------------------------------- 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 : 11.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.013 0.001 TRP I 146 HIS 0.003 0.001 HIS I 202 PHE 0.011 0.001 PHE I 131 TYR 0.011 0.001 TYR K 190 ARG 0.004 0.000 ARG L 137 Details of bonding type rmsd hydrogen bonds : bond 0.15044 ( 800) hydrogen bonds : angle 5.24118 ( 2277) metal coordination : bond 0.34279 ( 8) metal coordination : angle 4.82504 ( 6) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.75018 ( 4) covalent geometry : bond 0.00738 (16910) covalent geometry : angle 0.70128 (23099) 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 : 1.802 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: 1.6173 time to fit residues: 378.4936 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 : 1.814 ------------------------------------------------------------------------------- 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 155 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.091888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.055692 restraints weight = 25641.837| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.00 r_work: 0.2548 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 16931 Z= 0.161 Angle : 0.715 11.588 23109 Z= 0.327 Chirality : 0.047 0.181 2572 Planarity : 0.005 0.047 2761 Dihedral : 17.502 112.065 3117 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.18 % Allowed : 17.23 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1902 helix: 2.49 (0.17), residues: 960 sheet: -0.05 (0.35), residues: 200 loop : -1.31 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.004 0.001 HIS L 72 PHE 0.020 0.001 PHE A 52 TYR 0.014 0.001 TYR K 190 ARG 0.005 0.000 ARG L 137 Details of bonding type rmsd hydrogen bonds : bond 0.08470 ( 800) hydrogen bonds : angle 3.98425 ( 2277) metal coordination : bond 0.01084 ( 8) metal coordination : angle 4.02187 ( 6) SS BOND : bond 0.00437 ( 2) SS BOND : angle 1.44514 ( 4) covalent geometry : bond 0.00357 (16910) covalent geometry : angle 0.71242 (23099) Misc. bond : bond 0.06149 ( 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 231 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 179 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: C 184 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7586 (tmm160) REVERT: D 140 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8349 (tmm-80) REVERT: D 166 GLU cc_start: 0.7805 (mp0) cc_final: 0.7564 (OUTLIER) REVERT: D 168 ASP cc_start: 0.8380 (t0) cc_final: 0.8171 (t0) REVERT: F 36 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: K 184 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7982 (ttp80) REVERT: L 54 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8334 (mt) REVERT: L 140 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8335 (tmm-80) outliers start: 52 outliers final: 22 residues processed: 214 average time/residue: 1.6556 time to fit residues: 385.2985 Evaluate side-chains 210 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.749 ------------------------------------------------------------------------------- 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 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 126 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.092530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.056353 restraints weight = 25546.678| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.99 r_work: 0.2557 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16931 Z= 0.152 Angle : 0.669 11.239 23109 Z= 0.308 Chirality : 0.045 0.181 2572 Planarity : 0.005 0.051 2761 Dihedral : 15.410 94.203 3098 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.93 % Allowed : 17.65 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1902 helix: 2.52 (0.17), residues: 967 sheet: 0.10 (0.35), residues: 206 loop : -1.31 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.015 0.001 PHE J 160 TYR 0.011 0.001 TYR K 190 ARG 0.005 0.000 ARG L 137 Details of bonding type rmsd hydrogen bonds : bond 0.08147 ( 800) hydrogen bonds : angle 3.84793 ( 2277) metal coordination : bond 0.00845 ( 8) metal coordination : angle 3.04942 ( 6) SS BOND : bond 0.00433 ( 2) SS BOND : angle 1.27515 ( 4) covalent geometry : bond 0.00342 (16910) covalent geometry : angle 0.66716 (23099) Misc. bond : bond 0.05915 ( 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 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: C 54 ASP cc_start: 0.8503 (t0) cc_final: 0.8287 (t0) REVERT: C 154 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8067 (pmm150) REVERT: F 36 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: G 3 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8356 (mm-30) REVERT: I 131 PHE cc_start: 0.9165 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: J 152 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8650 (p0) REVERT: K 54 ASP cc_start: 0.8558 (t0) cc_final: 0.8269 (t0) REVERT: K 154 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8072 (pmm150) REVERT: L 168 ASP cc_start: 0.8460 (t0) cc_final: 0.8231 (t0) REVERT: O 3 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8382 (mm-30) REVERT: O 31 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7653 (ttp-170) REVERT: R 43 THR cc_start: 0.8079 (p) cc_final: 0.7840 (p) outliers start: 48 outliers final: 21 residues processed: 217 average time/residue: 1.6166 time to fit residues: 382.6151 Evaluate side-chains 210 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 35 GLU Chi-restraints excluded: chain F residue 36 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 50 optimal weight: 2.9990 chunk 96 optimal weight: 0.0970 chunk 161 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 183 optimal weight: 0.0030 chunk 120 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.093972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057804 restraints weight = 25865.843| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.00 r_work: 0.2595 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1435 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= 0.138 Angle : 0.640 10.144 23109 Z= 0.295 Chirality : 0.045 0.270 2572 Planarity : 0.005 0.050 2761 Dihedral : 14.333 89.251 3098 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.38 % Allowed : 18.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1902 helix: 2.71 (0.17), residues: 957 sheet: 0.24 (0.35), residues: 206 loop : -1.26 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.004 0.001 HIS A 202 PHE 0.014 0.001 PHE A 52 TYR 0.009 0.001 TYR K 190 ARG 0.007 0.000 ARG L 137 Details of bonding type rmsd hydrogen bonds : bond 0.07255 ( 800) hydrogen bonds : angle 3.70441 ( 2277) metal coordination : bond 0.00575 ( 8) metal coordination : angle 3.21127 ( 6) SS BOND : bond 0.00336 ( 2) SS BOND : angle 1.09112 ( 4) covalent geometry : bond 0.00305 (16910) covalent geometry : angle 0.63834 (23099) Misc. bond : bond 0.05739 ( 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 216 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8720 (m-80) REVERT: C 54 ASP cc_start: 0.8526 (t0) cc_final: 0.8254 (t0) REVERT: C 283 MET cc_start: 0.8123 (tpp) cc_final: 0.7905 (tpt) REVERT: D 137 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7498 (mtm-85) REVERT: F 36 GLU cc_start: 0.8753 (pm20) cc_final: 0.8320 (pm20) REVERT: G 3 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8351 (mm-30) REVERT: I 131 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: K 184 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7835 (tmm-80) REVERT: L 32 TYR cc_start: 0.8413 (m-80) cc_final: 0.7772 (t80) REVERT: L 168 ASP cc_start: 0.8468 (t0) cc_final: 0.8256 (t0) REVERT: O 3 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8370 (mm-30) outliers start: 39 outliers final: 20 residues processed: 204 average time/residue: 1.7046 time to fit residues: 377.6543 Evaluate side-chains 204 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 131 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 35 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 56 PHE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 144 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.092612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056065 restraints weight = 25953.501| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.00 r_work: 0.2555 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 16931 Z= 0.156 Angle : 0.661 11.332 23109 Z= 0.306 Chirality : 0.046 0.336 2572 Planarity : 0.005 0.051 2761 Dihedral : 13.690 89.163 3091 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.69 % Allowed : 18.20 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1902 helix: 2.62 (0.17), residues: 961 sheet: 0.28 (0.34), residues: 206 loop : -1.22 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.005 0.001 HIS I 202 PHE 0.014 0.001 PHE I 52 TYR 0.009 0.001 TYR K 190 ARG 0.007 0.000 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.08264 ( 800) hydrogen bonds : angle 3.78051 ( 2277) metal coordination : bond 0.00678 ( 8) metal coordination : angle 2.59314 ( 6) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.38055 ( 4) covalent geometry : bond 0.00352 (16910) covalent geometry : angle 0.65967 (23099) Misc. bond : bond 0.06144 ( 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 233 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8495 (t0) cc_final: 0.8207 (t0) REVERT: D 67 GLU cc_start: 0.9282 (mp0) cc_final: 0.8941 (pm20) REVERT: D 137 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7577 (mtm-85) REVERT: D 173 GLU cc_start: 0.8902 (pt0) cc_final: 0.8409 (pm20) REVERT: F 36 GLU cc_start: 0.8698 (pm20) cc_final: 0.8250 (pm20) REVERT: G 3 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: G 31 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7638 (ttp-170) REVERT: K 54 ASP cc_start: 0.8563 (t0) cc_final: 0.8249 (t0) REVERT: K 184 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7847 (tmm-80) REVERT: K 222 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8464 (tppt) REVERT: L 32 TYR cc_start: 0.8420 (m-80) cc_final: 0.7799 (t80) REVERT: L 168 ASP cc_start: 0.8471 (t0) cc_final: 0.8256 (t0) REVERT: O 3 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8365 (mm-30) REVERT: O 31 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7837 (ttp-170) outliers start: 44 outliers final: 24 residues processed: 211 average time/residue: 1.6716 time to fit residues: 383.4997 Evaluate side-chains 211 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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 151 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 G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG 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 L residue 120 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.093988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.057803 restraints weight = 26003.567| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.01 r_work: 0.2594 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1568 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= 0.138 Angle : 0.630 10.148 23109 Z= 0.292 Chirality : 0.045 0.309 2572 Planarity : 0.005 0.050 2761 Dihedral : 13.192 89.816 3090 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.50 % Allowed : 18.45 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1902 helix: 2.72 (0.17), residues: 957 sheet: 0.26 (0.34), residues: 211 loop : -1.19 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.001 PHE A 52 TYR 0.008 0.001 TYR K 53 ARG 0.006 0.000 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.07272 ( 800) hydrogen bonds : angle 3.69096 ( 2277) metal coordination : bond 0.00539 ( 8) metal coordination : angle 2.91523 ( 6) SS BOND : bond 0.00323 ( 2) SS BOND : angle 1.05345 ( 4) covalent geometry : bond 0.00301 (16910) covalent geometry : angle 0.62803 (23099) Misc. bond : bond 0.05990 ( 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 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8684 (m-80) REVERT: C 54 ASP cc_start: 0.8504 (t0) cc_final: 0.8206 (t0) REVERT: C 180 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8372 (mptt) REVERT: D 67 GLU cc_start: 0.9295 (mp0) cc_final: 0.8952 (pm20) REVERT: D 137 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7571 (mtm-85) REVERT: D 173 GLU cc_start: 0.8917 (pt0) cc_final: 0.8430 (pm20) REVERT: I 131 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: K 54 ASP cc_start: 0.8563 (t0) cc_final: 0.8244 (t0) REVERT: K 222 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8509 (ptmm) REVERT: L 32 TYR cc_start: 0.8398 (m-80) cc_final: 0.7789 (t80) REVERT: L 168 ASP cc_start: 0.8437 (t0) cc_final: 0.8184 (t0) REVERT: O 31 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7672 (ttp-170) outliers start: 41 outliers final: 23 residues processed: 212 average time/residue: 1.6703 time to fit residues: 384.8333 Evaluate side-chains 208 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 131 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 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 I residue 56 PHE Chi-restraints excluded: chain I residue 131 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 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 120 GLU 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 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 161 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 125 optimal weight: 0.0570 chunk 131 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 4.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.098196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063095 restraints weight = 26116.682| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.00 r_work: 0.2711 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1921 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= 0.118 Angle : 0.582 8.847 23109 Z= 0.272 Chirality : 0.043 0.220 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.359 89.708 3090 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.26 % Allowed : 18.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 1902 helix: 2.86 (0.17), residues: 959 sheet: 0.30 (0.32), residues: 221 loop : -1.12 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.002 0.001 HIS A 202 PHE 0.011 0.001 PHE I 131 TYR 0.009 0.001 TYR K 53 ARG 0.008 0.000 ARG M 29 Details of bonding type rmsd hydrogen bonds : bond 0.05232 ( 800) hydrogen bonds : angle 3.46886 ( 2277) metal coordination : bond 0.00336 ( 8) metal coordination : angle 3.44855 ( 6) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.64139 ( 4) covalent geometry : bond 0.00253 (16910) covalent geometry : angle 0.57941 (23099) Misc. bond : bond 0.05074 ( 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 230 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8488 (t0) cc_final: 0.8191 (t0) REVERT: D 67 GLU cc_start: 0.9312 (mp0) cc_final: 0.8999 (pm20) REVERT: D 137 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7501 (mtm-85) REVERT: D 173 GLU cc_start: 0.8964 (pt0) cc_final: 0.8454 (pm20) REVERT: J 152 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8632 (p0) REVERT: K 54 ASP cc_start: 0.8542 (t0) cc_final: 0.8220 (t0) REVERT: K 194 ILE cc_start: 0.9211 (pp) cc_final: 0.8900 (mp) REVERT: L 32 TYR cc_start: 0.8371 (m-80) cc_final: 0.7792 (t80) REVERT: L 140 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7738 (tpt-90) REVERT: L 168 ASP cc_start: 0.8395 (t0) cc_final: 0.8191 (t0) outliers start: 37 outliers final: 19 residues processed: 215 average time/residue: 1.7235 time to fit residues: 405.7900 Evaluate side-chains 211 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 167 GLU 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 13 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 25 LEU 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 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain R residue 52 ASP 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 79 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 165 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 overall best weight: 0.9960 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.094748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058782 restraints weight = 25631.662| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 1.98 r_work: 0.2614 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1772 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= 0.136 Angle : 0.621 10.245 23109 Z= 0.288 Chirality : 0.044 0.177 2572 Planarity : 0.005 0.050 2761 Dihedral : 12.332 89.352 3088 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.59 % Allowed : 19.79 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), residues: 1902 helix: 2.81 (0.17), residues: 957 sheet: 0.34 (0.32), residues: 221 loop : -1.06 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.001 PHE A 52 TYR 0.012 0.001 TYR R 49 ARG 0.006 0.000 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.07038 ( 800) hydrogen bonds : angle 3.57472 ( 2277) metal coordination : bond 0.00626 ( 8) metal coordination : angle 2.63155 ( 6) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.13314 ( 4) covalent geometry : bond 0.00306 (16910) covalent geometry : angle 0.61902 (23099) Misc. bond : bond 0.05474 ( 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 219 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8544 (t0) cc_final: 0.8220 (t0) REVERT: D 67 GLU cc_start: 0.9314 (mp0) cc_final: 0.9005 (pm20) REVERT: D 137 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7566 (mtm-85) REVERT: D 173 GLU cc_start: 0.8963 (pt0) cc_final: 0.8450 (pm20) REVERT: G 3 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8281 (mm-30) REVERT: K 54 ASP cc_start: 0.8552 (t0) cc_final: 0.8208 (t0) REVERT: K 194 ILE cc_start: 0.9323 (pp) cc_final: 0.8894 (mp) REVERT: L 32 TYR cc_start: 0.8362 (m-80) cc_final: 0.7751 (t80) REVERT: L 140 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7847 (tpt-90) REVERT: L 168 ASP cc_start: 0.8404 (t0) cc_final: 0.8175 (t0) REVERT: O 3 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: O 31 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7603 (ttm110) REVERT: O 33 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.6085 (m-30) outliers start: 26 outliers final: 18 residues processed: 208 average time/residue: 1.6323 time to fit residues: 369.4960 Evaluate side-chains 205 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 167 GLU 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 G residue 3 GLU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain I residue 56 PHE 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 L residue 120 GLU Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 33 ASP Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain R residue 52 ASP 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 176 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 178 optimal weight: 0.0060 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.096000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.060263 restraints weight = 26034.534| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.00 r_work: 0.2648 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1857 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= 0.124 Angle : 0.599 9.851 23109 Z= 0.280 Chirality : 0.043 0.162 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.049 89.821 3088 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.65 % Allowed : 19.67 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1902 helix: 2.86 (0.17), residues: 954 sheet: 0.35 (0.32), residues: 221 loop : -1.00 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.004 0.001 HIS A 202 PHE 0.011 0.001 PHE A 52 TYR 0.010 0.001 TYR R 49 ARG 0.008 0.000 ARG E 29 Details of bonding type rmsd hydrogen bonds : bond 0.06273 ( 800) hydrogen bonds : angle 3.51894 ( 2277) metal coordination : bond 0.00482 ( 8) metal coordination : angle 2.99700 ( 6) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.87294 ( 4) covalent geometry : bond 0.00271 (16910) covalent geometry : angle 0.59735 (23099) Misc. bond : bond 0.05450 ( 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 212 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: C 54 ASP cc_start: 0.8552 (t0) cc_final: 0.8238 (t0) REVERT: D 67 GLU cc_start: 0.9317 (mp0) cc_final: 0.9015 (pm20) REVERT: D 137 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7523 (mtm-85) REVERT: D 173 GLU cc_start: 0.8967 (pt0) cc_final: 0.8452 (pm20) REVERT: G 3 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: K 54 ASP cc_start: 0.8557 (t0) cc_final: 0.8214 (t0) REVERT: K 184 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7551 (mmp80) REVERT: K 194 ILE cc_start: 0.9355 (pp) cc_final: 0.8931 (mp) REVERT: L 32 TYR cc_start: 0.8360 (m-80) cc_final: 0.7759 (t80) REVERT: L 140 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7822 (tpt-90) REVERT: L 168 ASP cc_start: 0.8396 (t0) cc_final: 0.8169 (t0) REVERT: O 3 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8287 (mm-30) REVERT: O 31 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7541 (ttm110) outliers start: 27 outliers final: 19 residues processed: 201 average time/residue: 1.6356 time to fit residues: 357.6130 Evaluate side-chains 206 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 167 GLU 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 G residue 3 GLU Chi-restraints excluded: chain G residue 33 ASP 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 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain P residue 3 ILE 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 110 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 135 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.091495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.054753 restraints weight = 25728.706| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.01 r_work: 0.2523 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 16931 Z= 0.194 Angle : 0.705 14.346 23109 Z= 0.331 Chirality : 0.047 0.158 2572 Planarity : 0.005 0.049 2761 Dihedral : 12.560 88.699 3088 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.41 % Allowed : 19.91 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 1902 helix: 2.53 (0.17), residues: 961 sheet: 0.28 (0.32), residues: 216 loop : -1.05 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.006 0.001 HIS A 202 PHE 0.016 0.002 PHE C 128 TYR 0.013 0.002 TYR Q 49 ARG 0.008 0.001 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.09410 ( 800) hydrogen bonds : angle 3.81850 ( 2277) metal coordination : bond 0.00771 ( 8) metal coordination : angle 2.27341 ( 6) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.71095 ( 4) covalent geometry : bond 0.00471 (16910) covalent geometry : angle 0.70405 (23099) Misc. bond : bond 0.07052 ( 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 206 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.920 Fit side-chains REVERT: C 54 ASP cc_start: 0.8567 (t0) cc_final: 0.8247 (t0) REVERT: D 67 GLU cc_start: 0.9310 (mp0) cc_final: 0.9000 (pm20) REVERT: D 137 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7641 (mtm-85) REVERT: D 173 GLU cc_start: 0.8938 (pt0) cc_final: 0.8439 (pm20) REVERT: K 54 ASP cc_start: 0.8596 (t0) cc_final: 0.8291 (t0) REVERT: K 182 ILE cc_start: 0.8301 (pt) cc_final: 0.7857 (pp) REVERT: K 194 ILE cc_start: 0.9355 (pp) cc_final: 0.8917 (mp) REVERT: L 32 TYR cc_start: 0.8435 (m-80) cc_final: 0.7775 (t80) REVERT: L 168 ASP cc_start: 0.8407 (t0) cc_final: 0.8168 (t0) REVERT: O 3 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: O 31 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7902 (ttp-170) outliers start: 23 outliers final: 13 residues processed: 196 average time/residue: 1.7163 time to fit residues: 365.0248 Evaluate side-chains 195 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU 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 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 O residue 3 GLU 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 34 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 154 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 chunk 5 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.096207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.060679 restraints weight = 25928.812| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.00 r_work: 0.2639 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1876 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= 0.125 Angle : 0.610 10.030 23109 Z= 0.287 Chirality : 0.043 0.158 2572 Planarity : 0.005 0.053 2761 Dihedral : 11.967 89.783 3088 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.98 % Allowed : 20.40 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1902 helix: 2.78 (0.17), residues: 954 sheet: 0.26 (0.32), residues: 216 loop : -0.99 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.003 0.001 HIS I 202 PHE 0.010 0.001 PHE A 52 TYR 0.010 0.001 TYR R 49 ARG 0.011 0.001 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.06071 ( 800) hydrogen bonds : angle 3.57465 ( 2277) metal coordination : bond 0.00323 ( 8) metal coordination : angle 3.39790 ( 6) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.74235 ( 4) covalent geometry : bond 0.00273 (16910) covalent geometry : angle 0.60781 (23099) Misc. bond : bond 0.05474 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21732.30 seconds wall clock time: 375 minutes 15.83 seconds (22515.83 seconds total)