Starting phenix.real_space_refine on Sat Jul 4 05:21:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qrm_14123/07_2026/7qrm_14123_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qrm_14123/07_2026/7qrm_14123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qrm_14123/07_2026/7qrm_14123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qrm_14123/07_2026/7qrm_14123.map" model { file = "/net/cci-nas-00/data/ceres_data/7qrm_14123/07_2026/7qrm_14123_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qrm_14123/07_2026/7qrm_14123_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 10966 2.51 5 N 2446 2.21 5 O 2834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16336 Number of models: 1 Model: "" Number of chains: 27 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: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} Chain: "D" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 13, 'TRANS': 153} 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: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} 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: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} 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: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} 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: "A" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 368 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PGT': 1, 'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 164 Unusual residues: {'FES': 1, 'PGT': 1, 'PL9': 1, 'SQD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 358 Unusual residues: {'HEC': 1, 'HEM': 2, 'PGT': 1, 'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 243 Unusual residues: {'CLA': 1, 'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'HEC': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'FES': 1, 'PGT': 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 5839 SG CYS D 107 73.756 42.153 44.406 1.00 48.10 S ATOM 5975 SG CYS D 125 70.332 41.349 42.903 1.00 48.21 S ATOM 13208 SG CYS L 107 30.877 42.976 95.378 1.00 50.53 S ATOM 13344 SG CYS L 125 34.211 42.063 96.898 1.00 48.29 S Time building chain proxies: 4.30, per 1000 atoms: 0.26 Number of scatterers: 16336 At special positions: 0 Unit cell: (102.34, 121.26, 140.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 72 16.00 P 4 15.00 Mg 2 11.99 O 2834 8.00 N 2446 7.00 C 10966 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=2.04 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 597.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 203 " pdb="FE1 FES D 203 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 203 " - pdb=" SG CYS D 125 " pdb="FE2 FES D 203 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 203 " - pdb=" ND1 HIS D 109 " pdb=" FES L 802 " pdb="FE1 FES L 802 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 802 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 802 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 802 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3478 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 16 sheets defined 50.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.566A pdb=" N TRP A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.621A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 106 removed outlier: 3.655A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 removed outlier: 3.828A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.669A pdb=" N ILE A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.621A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.539A pdb=" N LEU A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.660A pdb=" N LEU A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 removed outlier: 3.549A pdb=" N LYS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 removed outlier: 3.517A 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 109 removed outlier: 4.182A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 146 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 155 removed outlier: 4.584A pdb=" N LEU B 155 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.562A pdb=" N ILE C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 26 Processing helix chain 'D' and resid 26 through 41 removed outlier: 4.284A pdb=" N THR D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Proline residue: D 36 - end of helix removed outlier: 4.105A pdb=" N PHE D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 71 removed outlier: 3.544A pdb=" N THR D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 26 Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.514A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 9 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 11 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 12 " --> pdb=" O ARG F 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 31 removed outlier: 3.868A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix removed outlier: 3.592A pdb=" N ARG G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.754A pdb=" N LEU H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA H 7 " --> pdb=" O ILE H 3 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 13 removed outlier: 3.808A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 removed outlier: 3.650A 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: 3.701A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.978A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.820A pdb=" N ILE I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 152 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 157 removed outlier: 3.948A pdb=" N ALA I 157 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 171 Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 removed outlier: 3.701A 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: 3.540A 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: 4.217A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.799A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 removed outlier: 3.650A pdb=" N LEU J 114 " --> pdb=" O VAL J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 removed outlier: 3.684A pdb=" N THR J 130 " --> pdb=" O ARG J 126 " (cutoff:3.500A) 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 removed outlier: 4.066A pdb=" N SER J 154 " --> pdb=" O ILE J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 removed outlier: 3.705A pdb=" N ASN K 23 " --> pdb=" O VAL K 20 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS K 24 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.615A pdb=" N ILE K 89 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.691A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.655A pdb=" N LYS K 138 " --> pdb=" O PRO K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.607A pdb=" N ILE K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE K 256 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE K 257 " --> pdb=" O GLY K 253 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS K 273 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 40 removed outlier: 3.726A pdb=" N THR L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix removed outlier: 3.604A 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 35 removed outlier: 3.866A pdb=" N PHE N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR N 17 " --> pdb=" O MET N 13 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 30 removed outlier: 3.855A 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: 3.733A pdb=" N LEU P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL P 22 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL P 23 " --> pdb=" O LEU P 19 " (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: 3.863A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.565A pdb=" N GLY C 67 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.181A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY C 72 " --> pdb=" O ASN C 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 104 removed outlier: 6.181A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 177 through 184 removed outlier: 5.487A pdb=" N VAL C 179 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 195 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 181 " --> pdb=" O ASN C 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.713A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 103 " --> pdb=" O TYR D 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 123 through 124 removed outlier: 6.745A pdb=" N GLN D 131 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AB1, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.785A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 38 through 39 removed outlier: 3.545A pdb=" N TYR K 149 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 38 through 39 removed outlier: 3.545A pdb=" N TYR K 149 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY K 72 " --> pdb=" O ASN K 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB5, first strand: chain 'K' and resid 202 through 207 removed outlier: 6.736A pdb=" N GLU K 191 " --> pdb=" O ILE K 182 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE K 182 " --> pdb=" O GLU K 191 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASN K 193 " --> pdb=" O LYS K 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.628A pdb=" N ALA L 150 " --> pdb=" O GLY L 102 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS L 152 " --> pdb=" O THR L 100 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR L 100 " --> pdb=" O CYS L 152 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N VAL L 154 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N LEU L 98 " --> pdb=" O VAL L 154 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE L 103 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 122 through 124 removed outlier: 6.190A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) 735 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6272 1.39 - 1.59: 10340 1.59 - 1.80: 57 1.80 - 2.00: 65 2.00 - 2.20: 48 Bond restraints: 16782 Sorted by residual: bond pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " ideal model delta sigma weight residual 1.334 1.466 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C2A HEC A 303 " pdb=" C3A HEC A 303 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C1 SQD D 201 " pdb=" O5 SQD D 201 " ideal model delta sigma weight residual 1.500 1.397 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 SQD K 302 " pdb=" O5 SQD K 302 " ideal model delta sigma weight residual 1.500 1.399 0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 16777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 22569 3.39 - 6.77: 271 6.77 - 10.16: 33 10.16 - 13.54: 2 13.54 - 16.93: 4 Bond angle restraints: 22879 Sorted by residual: angle pdb=" N LEU A 12 " pdb=" CA LEU A 12 " pdb=" C LEU A 12 " ideal model delta sigma weight residual 112.88 121.45 -8.57 1.29e+00 6.01e-01 4.41e+01 angle pdb=" N ASN B 34 " pdb=" CA ASN B 34 " pdb=" C ASN B 34 " ideal model delta sigma weight residual 111.02 118.15 -7.13 1.22e+00 6.72e-01 3.41e+01 angle pdb=" O3P PGT D 204 " pdb=" P PGT D 204 " pdb=" O4P PGT D 204 " ideal model delta sigma weight residual 92.82 109.75 -16.93 3.00e+00 1.11e-01 3.18e+01 angle pdb=" O3P PGT L 801 " pdb=" P PGT L 801 " pdb=" O4P PGT L 801 " ideal model delta sigma weight residual 92.82 109.48 -16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O3P PGT A 308 " pdb=" P PGT A 308 " pdb=" O4P PGT A 308 " ideal model delta sigma weight residual 92.82 109.36 -16.54 3.00e+00 1.11e-01 3.04e+01 ... (remaining 22874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.52: 9231 25.52 - 51.03: 646 51.03 - 76.55: 141 76.55 - 102.07: 53 102.07 - 127.58: 20 Dihedral angle restraints: 10091 sinusoidal: 4667 harmonic: 5424 Sorted by residual: dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 0.13 59.87 2 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " pdb=" CAB HEC A 303 " pdb=" CBB HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 0.17 59.83 2 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA PRO A 159 " pdb=" C PRO A 159 " pdb=" N VAL A 160 " pdb=" CA VAL A 160 " ideal model delta harmonic sigma weight residual 180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 10088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2144 0.069 - 0.138: 332 0.138 - 0.207: 35 0.207 - 0.276: 8 0.276 - 0.345: 4 Chirality restraints: 2523 Sorted by residual: 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 -2.04 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA LEU A 12 " pdb=" N LEU A 12 " pdb=" C LEU A 12 " pdb=" CB LEU A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN B 34 " pdb=" N ASN B 34 " pdb=" C ASN B 34 " pdb=" CB ASN B 34 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2520 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.149 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" C21 BCR P 101 " -0.208 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " -0.026 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.105 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR F 101 " -0.128 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C23 BCR F 101 " 0.116 2.00e-02 2.50e+03 pdb=" C24 BCR F 101 " 0.146 2.00e-02 2.50e+03 pdb=" C25 BCR F 101 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR P 101 " -0.103 2.00e-02 2.50e+03 1.05e-01 1.10e+02 pdb=" C23 BCR P 101 " 0.098 2.00e-02 2.50e+03 pdb=" C24 BCR P 101 " 0.111 2.00e-02 2.50e+03 pdb=" C25 BCR P 101 " -0.106 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 115 2.61 - 3.18: 13290 3.18 - 3.75: 22266 3.75 - 4.33: 33035 4.33 - 4.90: 55610 Nonbonded interactions: 124316 Sorted by model distance: nonbonded pdb=" O2 UMQ J 205 " pdb=" O3' UMQ J 205 " model vdw 2.033 3.040 nonbonded pdb=" O PHE A 52 " pdb=" OG1 THR A 55 " model vdw 2.128 3.040 nonbonded pdb=" O GLN C 37 " pdb=" O6 UMQ H 201 " model vdw 2.138 3.040 nonbonded pdb=" O ALA L 99 " pdb=" OG1 THR L 100 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLU L 173 " pdb=" N ALA L 174 " model vdw 2.194 3.120 ... (remaining 124311 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 302 or resid 306)) selection = (chain 'I' and (resid 2 through 215 or resid 2002 or resid 2006)) } ncs_group { reference = (chain 'B' and resid 2 through 160) 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 )))) } ncs_group { reference = chain 'C' selection = (chain 'K' and resid 1 through 301) } ncs_group { reference = (chain 'D' and (resid 8 through 51 or resid 53 through 178)) selection = (chain 'L' and resid 8 through 178) } 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' 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)))) } 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: 6.650 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.030 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 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:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 0.462 16801 Z= 0.452 Angle : 0.912 16.931 22889 Z= 0.438 Chirality : 0.052 0.345 2523 Planarity : 0.008 0.132 2711 Dihedral : 19.607 127.581 6607 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.88 % Allowed : 1.19 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 1866 helix: 1.10 (0.18), residues: 905 sheet: -1.02 (0.32), residues: 215 loop : -2.00 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 126 TYR 0.017 0.001 TYR A 136 PHE 0.031 0.002 PHE A 56 TRP 0.012 0.001 TRP I 146 HIS 0.009 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.43 (16782) covalent geometry : angle 0.91033 / 0.44 (22879) SS BOND : bond 0.00394 / 0.19 ( 2) SS BOND : angle 1.31149 / 0.62 ( 4) hydrogen bonds : bond 0.16683 / 10.80 ( 721) hydrogen bonds : angle 5.58241 / 4.01 ( 2103) metal coordination : bond 0.31614 / 18.14 ( 8) metal coordination : angle 3.90582 / 2.15 ( 6) Misc. bond : bond 0.32607 / 20.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.623 Fit side-chains REVERT: A 13 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 5 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7648 (tttp) REVERT: B 15 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7163 (mtp85) REVERT: E 27 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8139 (tptt) REVERT: E 29 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6625 (mmp-170) REVERT: J 119 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7795 (tttm) REVERT: K 103 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7495 (mm-40) outliers start: 30 outliers final: 7 residues processed: 217 average time/residue: 0.6059 time to fit residues: 144.6751 Evaluate side-chains 179 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 116 ASN C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102583 restraints weight = 19050.891| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.38 r_work: 0.2927 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 16801 Z= 0.144 Angle : 0.703 16.946 22889 Z= 0.315 Chirality : 0.047 0.203 2523 Planarity : 0.005 0.057 2711 Dihedral : 18.442 105.154 3238 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.82 % Allowed : 7.08 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1866 helix: 1.73 (0.18), residues: 917 sheet: -0.56 (0.34), residues: 201 loop : -1.78 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 30 TYR 0.012 0.001 TYR A 136 PHE 0.020 0.001 PHE A 131 TRP 0.009 0.001 TRP A 118 HIS 0.008 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (16782) covalent geometry : angle 0.69889 / 0.32 (22879) SS BOND : bond 0.00386 / 0.19 ( 2) SS BOND : angle 1.31631 / 0.65 ( 4) hydrogen bonds : bond 0.06898 / 4.64 ( 721) hydrogen bonds : angle 4.08668 / 2.95 ( 2103) metal coordination : bond 0.01108 / 0.59 ( 8) metal coordination : angle 4.87345 / 2.99 ( 6) Misc. bond : bond 0.08053 / 5.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.638 Fit side-chains REVERT: A 13 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8416 (mt-10) REVERT: A 64 ASP cc_start: 0.8385 (m-30) cc_final: 0.8089 (m-30) REVERT: B 5 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7366 (tttp) REVERT: B 15 ARG cc_start: 0.7660 (mtm-85) cc_final: 0.7095 (mtp85) REVERT: B 119 LYS cc_start: 0.7534 (pmtt) cc_final: 0.6906 (tptm) REVERT: D 35 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7832 (mp) REVERT: E 27 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7950 (tptt) REVERT: F 8 ARG cc_start: 0.8232 (ttp-170) cc_final: 0.8014 (ttp80) REVERT: F 29 ARG cc_start: 0.7698 (tpp-160) cc_final: 0.7314 (tpm170) REVERT: I 13 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7670 (mm-30) REVERT: I 96 MET cc_start: 0.9257 (mmt) cc_final: 0.9049 (mmt) REVERT: K 103 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: K 184 ARG cc_start: 0.6927 (mpt180) cc_final: 0.6284 (ttm-80) REVERT: L 122 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8181 (ptpp) outliers start: 29 outliers final: 13 residues processed: 192 average time/residue: 0.6429 time to fit residues: 135.4222 Evaluate side-chains 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 15 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104712 restraints weight = 19115.116| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.33 r_work: 0.2961 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.183 16801 Z= 0.127 Angle : 0.648 15.909 22889 Z= 0.287 Chirality : 0.046 0.274 2523 Planarity : 0.005 0.056 2711 Dihedral : 15.959 90.716 3217 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.57 % Allowed : 9.34 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1866 helix: 2.07 (0.18), residues: 925 sheet: -0.52 (0.33), residues: 228 loop : -1.55 (0.20), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 30 TYR 0.009 0.001 TYR A 136 PHE 0.018 0.001 PHE A 131 TRP 0.009 0.001 TRP A 118 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16782) covalent geometry : angle 0.64425 / 0.29 (22879) SS BOND : bond 0.00310 / 0.16 ( 2) SS BOND : angle 1.03612 / 0.52 ( 4) hydrogen bonds : bond 0.06024 / 4.07 ( 721) hydrogen bonds : angle 3.74907 / 2.70 ( 2103) metal coordination : bond 0.01021 / 0.56 ( 8) metal coordination : angle 4.12102 / 2.52 ( 6) Misc. bond : bond 0.07767 / 5.35 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.456 Fit side-chains REVERT: A 64 ASP cc_start: 0.8417 (m-30) cc_final: 0.8094 (m-30) REVERT: A 73 MET cc_start: 0.8801 (tpt) cc_final: 0.8541 (mmm) REVERT: B 5 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7386 (tttm) REVERT: B 6 LYS cc_start: 0.7873 (mmpt) cc_final: 0.7405 (mppt) REVERT: B 15 ARG cc_start: 0.7596 (mtm-85) cc_final: 0.7077 (mtp85) REVERT: B 119 LYS cc_start: 0.7478 (pmtt) cc_final: 0.7132 (mttp) REVERT: E 27 LYS cc_start: 0.8189 (tppt) cc_final: 0.7965 (tptt) REVERT: I 13 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7650 (mm-30) REVERT: I 73 MET cc_start: 0.8763 (mmm) cc_final: 0.8490 (mmt) REVERT: J 78 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7321 (mm-30) REVERT: J 119 LYS cc_start: 0.8767 (mptp) cc_final: 0.7424 (ttpm) REVERT: K 184 ARG cc_start: 0.6989 (mpt180) cc_final: 0.6761 (mpt180) REVERT: L 122 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8230 (ptpt) REVERT: M 29 ARG cc_start: 0.7731 (mpt180) cc_final: 0.7244 (mmm160) outliers start: 25 outliers final: 12 residues processed: 190 average time/residue: 0.6320 time to fit residues: 131.8376 Evaluate side-chains 182 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain N residue 33 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 144 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN C 153 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.103411 restraints weight = 18972.808| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.28 r_work: 0.2949 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 16801 Z= 0.129 Angle : 0.644 16.236 22889 Z= 0.284 Chirality : 0.045 0.325 2523 Planarity : 0.005 0.059 2711 Dihedral : 14.726 88.746 3207 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.13 % Allowed : 9.96 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1866 helix: 2.21 (0.17), residues: 925 sheet: -0.30 (0.33), residues: 228 loop : -1.41 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 30 TYR 0.010 0.001 TYR A 136 PHE 0.015 0.001 PHE A 131 TRP 0.008 0.001 TRP A 118 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16782) covalent geometry : angle 0.64095 / 0.28 (22879) SS BOND : bond 0.00331 / 0.16 ( 2) SS BOND : angle 1.10759 / 0.56 ( 4) hydrogen bonds : bond 0.06260 / 4.23 ( 721) hydrogen bonds : angle 3.66492 / 2.64 ( 2103) metal coordination : bond 0.00622 / 0.33 ( 8) metal coordination : angle 3.93660 / 2.40 ( 6) Misc. bond : bond 0.07594 / 5.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.427 Fit side-chains REVERT: A 20 ASP cc_start: 0.8593 (t70) cc_final: 0.8339 (t0) REVERT: A 64 ASP cc_start: 0.8421 (m-30) cc_final: 0.8095 (m-30) REVERT: B 5 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7457 (tttm) REVERT: B 15 ARG cc_start: 0.7599 (mtm-85) cc_final: 0.7102 (mtp85) REVERT: B 119 LYS cc_start: 0.7490 (pmtt) cc_final: 0.7202 (mttp) REVERT: E 27 LYS cc_start: 0.8165 (tppt) cc_final: 0.7951 (tptt) REVERT: G 30 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6344 (mtt-85) REVERT: I 13 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7643 (mm-30) REVERT: I 73 MET cc_start: 0.8805 (mmm) cc_final: 0.8585 (mmt) REVERT: J 119 LYS cc_start: 0.8783 (mptp) cc_final: 0.7395 (tttm) REVERT: K 184 ARG cc_start: 0.7054 (mpt180) cc_final: 0.6817 (mpt180) REVERT: L 122 LYS cc_start: 0.8438 (ptpt) cc_final: 0.8213 (ptpt) REVERT: M 29 ARG cc_start: 0.7710 (mpt90) cc_final: 0.7242 (mmm160) REVERT: O 3 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7508 (mt-10) outliers start: 34 outliers final: 12 residues processed: 191 average time/residue: 0.6342 time to fit residues: 132.5203 Evaluate side-chains 183 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 103 GLN K 6 GLN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098940 restraints weight = 18980.356| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.42 r_work: 0.2892 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 16801 Z= 0.150 Angle : 0.681 16.641 22889 Z= 0.301 Chirality : 0.047 0.374 2523 Planarity : 0.005 0.059 2711 Dihedral : 14.376 89.831 3205 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.13 % Allowed : 10.78 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.20), residues: 1866 helix: 2.11 (0.17), residues: 929 sheet: -0.21 (0.34), residues: 223 loop : -1.29 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 30 TYR 0.012 0.001 TYR A 136 PHE 0.015 0.002 PHE A 131 TRP 0.009 0.001 TRP A 118 HIS 0.009 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (16782) covalent geometry : angle 0.67764 / 0.30 (22879) SS BOND : bond 0.00485 / 0.24 ( 2) SS BOND : angle 1.45621 / 0.72 ( 4) hydrogen bonds : bond 0.07385 / 5.00 ( 721) hydrogen bonds : angle 3.72759 / 2.68 ( 2103) metal coordination : bond 0.00861 / 0.45 ( 8) metal coordination : angle 4.04577 / 2.47 ( 6) Misc. bond : bond 0.07579 / 5.17 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.578 Fit side-chains REVERT: A 64 ASP cc_start: 0.8477 (m-30) cc_final: 0.8210 (m-30) REVERT: A 73 MET cc_start: 0.8843 (tpt) cc_final: 0.8533 (mmm) REVERT: B 5 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7393 (tttp) REVERT: B 6 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7486 (mppt) REVERT: B 15 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.6948 (mtp85) REVERT: B 119 LYS cc_start: 0.7452 (pmtt) cc_final: 0.7175 (mttt) REVERT: G 30 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6407 (mtt-85) REVERT: I 13 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7677 (mm-30) REVERT: L 122 LYS cc_start: 0.8430 (ptpt) cc_final: 0.8178 (ptpt) REVERT: M 29 ARG cc_start: 0.7713 (mpt90) cc_final: 0.7271 (mmm160) outliers start: 34 outliers final: 18 residues processed: 188 average time/residue: 0.6229 time to fit residues: 128.3764 Evaluate side-chains 188 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 158 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 165 optimal weight: 0.0070 chunk 139 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102020 restraints weight = 19027.643| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.27 r_work: 0.2941 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 16801 Z= 0.140 Angle : 0.658 16.611 22889 Z= 0.291 Chirality : 0.046 0.382 2523 Planarity : 0.005 0.057 2711 Dihedral : 13.920 89.460 3205 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.13 % Allowed : 11.78 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1866 helix: 2.23 (0.17), residues: 925 sheet: -0.14 (0.34), residues: 223 loop : -1.27 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 30 TYR 0.010 0.001 TYR A 136 PHE 0.013 0.001 PHE A 198 TRP 0.008 0.001 TRP A 118 HIS 0.008 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16782) covalent geometry : angle 0.65449 / 0.29 (22879) SS BOND : bond 0.00413 / 0.21 ( 2) SS BOND : angle 1.30113 / 0.65 ( 4) hydrogen bonds : bond 0.06823 / 4.62 ( 721) hydrogen bonds : angle 3.67427 / 2.64 ( 2103) metal coordination : bond 0.00662 / 0.34 ( 8) metal coordination : angle 3.95676 / 2.41 ( 6) Misc. bond : bond 0.07441 / 5.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.575 Fit side-chains REVERT: A 20 ASP cc_start: 0.8584 (t70) cc_final: 0.8328 (t0) REVERT: A 64 ASP cc_start: 0.8482 (m-30) cc_final: 0.8228 (m-30) REVERT: A 73 MET cc_start: 0.8821 (tpt) cc_final: 0.8526 (mmm) REVERT: A 131 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: B 5 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7524 (tttm) REVERT: B 6 LYS cc_start: 0.8073 (mmmt) cc_final: 0.7502 (mppt) REVERT: B 15 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.6935 (mtp85) REVERT: B 119 LYS cc_start: 0.7451 (pmtt) cc_final: 0.7196 (mttt) REVERT: I 13 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7647 (mm-30) REVERT: I 131 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.6930 (t80) REVERT: J 119 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7405 (tttm) REVERT: L 122 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8170 (ptpt) REVERT: M 29 ARG cc_start: 0.7715 (mpt90) cc_final: 0.7287 (mmm160) REVERT: O 3 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7484 (mm-30) outliers start: 34 outliers final: 23 residues processed: 183 average time/residue: 0.6646 time to fit residues: 133.0536 Evaluate side-chains 191 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9980 chunk 102 optimal weight: 0.3980 chunk 125 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 175 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100724 restraints weight = 18943.222| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.26 r_work: 0.2914 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 16801 Z= 0.156 Angle : 0.687 16.790 22889 Z= 0.305 Chirality : 0.047 0.350 2523 Planarity : 0.005 0.058 2711 Dihedral : 13.941 89.879 3205 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.57 % Allowed : 11.84 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.19), residues: 1866 helix: 2.12 (0.17), residues: 929 sheet: -0.09 (0.34), residues: 217 loop : -1.23 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 30 TYR 0.012 0.001 TYR A 136 PHE 0.014 0.002 PHE A 198 TRP 0.009 0.001 TRP A 146 HIS 0.009 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (16782) covalent geometry : angle 0.68366 / 0.31 (22879) SS BOND : bond 0.00509 / 0.25 ( 2) SS BOND : angle 1.52388 / 0.75 ( 4) hydrogen bonds : bond 0.07585 / 5.14 ( 721) hydrogen bonds : angle 3.72165 / 2.68 ( 2103) metal coordination : bond 0.00881 / 0.46 ( 8) metal coordination : angle 3.96491 / 2.42 ( 6) Misc. bond : bond 0.07465 / 5.07 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.598 Fit side-chains REVERT: A 64 ASP cc_start: 0.8506 (m-30) cc_final: 0.8282 (m-30) REVERT: A 131 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: B 5 LYS cc_start: 0.7919 (ttpt) cc_final: 0.7551 (tttm) REVERT: B 15 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7000 (mtm110) REVERT: I 13 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7675 (mm-30) REVERT: J 78 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7573 (mm-30) REVERT: J 119 LYS cc_start: 0.8749 (mptp) cc_final: 0.7436 (tttm) REVERT: K 184 ARG cc_start: 0.7054 (mpt180) cc_final: 0.6452 (ttm-80) REVERT: M 29 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7303 (mmm160) outliers start: 41 outliers final: 27 residues processed: 189 average time/residue: 0.6333 time to fit residues: 131.1999 Evaluate side-chains 191 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 29 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 24 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 0.5980 chunk 140 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104286 restraints weight = 19069.820| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.26 r_work: 0.2955 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 16801 Z= 0.120 Angle : 0.611 16.284 22889 Z= 0.272 Chirality : 0.044 0.261 2523 Planarity : 0.005 0.057 2711 Dihedral : 13.312 88.817 3205 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.75 % Allowed : 12.91 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1866 helix: 2.43 (0.17), residues: 925 sheet: 0.03 (0.34), residues: 228 loop : -1.13 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 30 TYR 0.008 0.001 TYR J 80 PHE 0.012 0.001 PHE A 131 TRP 0.010 0.001 TRP A 118 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16782) covalent geometry : angle 0.60783 / 0.27 (22879) SS BOND : bond 0.00269 / 0.13 ( 2) SS BOND : angle 0.96841 / 0.49 ( 4) hydrogen bonds : bond 0.05729 / 3.87 ( 721) hydrogen bonds : angle 3.57520 / 2.57 ( 2103) metal coordination : bond 0.00504 / 0.26 ( 8) metal coordination : angle 3.81958 / 2.31 ( 6) Misc. bond : bond 0.07239 / 5.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.593 Fit side-chains REVERT: A 20 ASP cc_start: 0.8613 (t70) cc_final: 0.8371 (t0) REVERT: A 64 ASP cc_start: 0.8467 (m-30) cc_final: 0.8189 (m-30) REVERT: A 73 MET cc_start: 0.8808 (tpt) cc_final: 0.8538 (mmm) REVERT: A 131 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: B 5 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7564 (tttm) REVERT: B 6 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7477 (mppt) REVERT: B 15 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7031 (mtm110) REVERT: C 65 LYS cc_start: 0.7312 (mttt) cc_final: 0.6998 (mmtp) REVERT: C 110 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: I 13 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7704 (mm-30) REVERT: I 131 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7035 (t80) REVERT: J 119 LYS cc_start: 0.8649 (mptp) cc_final: 0.7397 (tttm) REVERT: K 184 ARG cc_start: 0.7020 (mpt180) cc_final: 0.6451 (ttm-80) REVERT: L 122 LYS cc_start: 0.8467 (ptpt) cc_final: 0.8259 (ptpt) REVERT: M 29 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7305 (mmm160) REVERT: P 1 MET cc_start: 0.5529 (pmm) cc_final: 0.5318 (ptt) outliers start: 28 outliers final: 19 residues processed: 185 average time/residue: 0.7017 time to fit residues: 142.0945 Evaluate side-chains 190 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain M residue 29 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 166 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106264 restraints weight = 18988.830| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.25 r_work: 0.3006 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 16801 Z= 0.115 Angle : 0.593 15.988 22889 Z= 0.265 Chirality : 0.043 0.189 2523 Planarity : 0.005 0.057 2711 Dihedral : 12.841 89.140 3205 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.75 % Allowed : 12.97 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 1866 helix: 2.55 (0.17), residues: 927 sheet: 0.25 (0.35), residues: 213 loop : -0.99 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 30 TYR 0.007 0.001 TYR J 80 PHE 0.015 0.001 PHE A 198 TRP 0.009 0.001 TRP A 118 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (16782) covalent geometry : angle 0.58968 / 0.26 (22879) SS BOND : bond 0.00243 / 0.12 ( 2) SS BOND : angle 0.91144 / 0.46 ( 4) hydrogen bonds : bond 0.05329 / 3.61 ( 721) hydrogen bonds : angle 3.47644 / 2.49 ( 2103) metal coordination : bond 0.00554 / 0.29 ( 8) metal coordination : angle 3.66085 / 2.21 ( 6) Misc. bond : bond 0.07317 / 5.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.634 Fit side-chains REVERT: A 20 ASP cc_start: 0.8571 (t70) cc_final: 0.8320 (t0) REVERT: A 64 ASP cc_start: 0.8413 (m-30) cc_final: 0.8105 (m-30) REVERT: A 73 MET cc_start: 0.8773 (tpt) cc_final: 0.8498 (mmm) REVERT: A 131 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: B 5 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7542 (tttm) REVERT: B 15 ARG cc_start: 0.7423 (mtm-85) cc_final: 0.6809 (mtp85) REVERT: B 119 LYS cc_start: 0.7338 (pmtt) cc_final: 0.7033 (tptm) REVERT: C 65 LYS cc_start: 0.7188 (mttt) cc_final: 0.6914 (mmtp) REVERT: I 13 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7581 (mm-30) REVERT: I 73 MET cc_start: 0.8745 (mmm) cc_final: 0.8459 (mmt) REVERT: I 131 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.6968 (t80) REVERT: J 119 LYS cc_start: 0.8629 (mptp) cc_final: 0.7339 (tttm) REVERT: K 184 ARG cc_start: 0.7139 (mpt180) cc_final: 0.6528 (ttm-80) REVERT: M 29 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7234 (mmm160) outliers start: 28 outliers final: 19 residues processed: 184 average time/residue: 0.6864 time to fit residues: 138.3792 Evaluate side-chains 192 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 29 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 140 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 127 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 0.0170 chunk 154 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.0030 overall best weight: 0.3026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 193 ASN L 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110796 restraints weight = 19114.420| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.25 r_work: 0.3064 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 16801 Z= 0.103 Angle : 0.558 15.404 22889 Z= 0.249 Chirality : 0.042 0.145 2523 Planarity : 0.005 0.058 2711 Dihedral : 12.330 88.709 3203 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.19 % Allowed : 13.78 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.20), residues: 1866 helix: 2.74 (0.17), residues: 927 sheet: 0.39 (0.34), residues: 222 loop : -0.92 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 30 TYR 0.008 0.001 TYR J 80 PHE 0.017 0.001 PHE A 198 TRP 0.009 0.001 TRP A 118 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (16782) covalent geometry : angle 0.55514 / 0.25 (22879) SS BOND : bond 0.00150 / 0.07 ( 2) SS BOND : angle 0.68588 / 0.35 ( 4) hydrogen bonds : bond 0.04213 / 2.85 ( 721) hydrogen bonds : angle 3.36009 / 2.40 ( 2103) metal coordination : bond 0.00454 / 0.24 ( 8) metal coordination : angle 3.39179 / 2.02 ( 6) Misc. bond : bond 0.06983 / 5.05 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.588 Fit side-chains REVERT: A 20 ASP cc_start: 0.8578 (t70) cc_final: 0.8316 (t0) REVERT: A 64 ASP cc_start: 0.8335 (m-30) cc_final: 0.8019 (m-30) REVERT: A 73 MET cc_start: 0.8781 (tpt) cc_final: 0.8472 (mmm) REVERT: A 131 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: B 5 LYS cc_start: 0.7941 (ttpt) cc_final: 0.7586 (tttm) REVERT: B 15 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.6885 (mtp85) REVERT: B 119 LYS cc_start: 0.7362 (pmtt) cc_final: 0.7114 (mttp) REVERT: C 65 LYS cc_start: 0.7093 (mttt) cc_final: 0.6829 (mmtp) REVERT: D 32 TYR cc_start: 0.7946 (m-80) cc_final: 0.7617 (m-10) REVERT: H 1 MET cc_start: 0.5260 (pmm) cc_final: 0.4570 (pmm) REVERT: I 13 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7600 (mm-30) REVERT: I 73 MET cc_start: 0.8725 (mmm) cc_final: 0.8507 (mmt) REVERT: I 131 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.7091 (t80) REVERT: I 165 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8357 (mt) REVERT: J 75 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7742 (tt) REVERT: J 119 LYS cc_start: 0.8622 (mptp) cc_final: 0.7358 (tttm) REVERT: K 103 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6846 (mp10) REVERT: K 184 ARG cc_start: 0.7189 (mpt180) cc_final: 0.6548 (ttm-80) REVERT: M 29 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7235 (mmm160) outliers start: 19 outliers final: 13 residues processed: 183 average time/residue: 0.6304 time to fit residues: 127.0178 Evaluate side-chains 185 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain M residue 29 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 115 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 13 GLN L 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107015 restraints weight = 18894.523| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.27 r_work: 0.3009 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.186 16801 Z= 0.118 Angle : 0.596 16.271 22889 Z= 0.266 Chirality : 0.043 0.143 2523 Planarity : 0.005 0.057 2711 Dihedral : 12.450 89.325 3203 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.38 % Allowed : 13.66 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.20), residues: 1866 helix: 2.63 (0.17), residues: 927 sheet: 0.43 (0.35), residues: 212 loop : -0.90 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 30 TYR 0.008 0.001 TYR J 80 PHE 0.015 0.001 PHE A 198 TRP 0.009 0.001 TRP A 146 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16782) covalent geometry : angle 0.59368 / 0.27 (22879) SS BOND : bond 0.00311 / 0.16 ( 2) SS BOND : angle 1.02653 / 0.52 ( 4) hydrogen bonds : bond 0.05437 / 3.68 ( 721) hydrogen bonds : angle 3.40568 / 2.44 ( 2103) metal coordination : bond 0.00529 / 0.28 ( 8) metal coordination : angle 3.38573 / 2.03 ( 6) Misc. bond : bond 0.07363 / 5.22 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5910.87 seconds wall clock time: 101 minutes 18.37 seconds (6078.37 seconds total)