Starting phenix.real_space_refine on Mon Jun 16 12:03:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qrm_14123/06_2025/7qrm_14123_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qrm_14123/06_2025/7qrm_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_14123/06_2025/7qrm_14123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qrm_14123/06_2025/7qrm_14123.map" model { file = "/net/cci-nas-00/data/ceres_data/7qrm_14123/06_2025/7qrm_14123_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qrm_14123/06_2025/7qrm_14123_trim.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.83, per 1000 atoms: 0.79 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: 5.63 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.89 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: 5.13 Time building geometry restraints manager: 6.01 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 - 33.19: 9577 33.19 - 66.38: 469 66.38 - 99.58: 77 99.58 - 132.77: 26 132.77 - 165.96: 2 Dihedral angle restraints: 10151 sinusoidal: 4727 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 10148 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 285 or resid 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: 3.750 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: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 47.750 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 20.049 165.960 6667 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (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 TRP 0.012 0.001 TRP I 146 HIS 0.009 0.001 HIS I 202 PHE 0.031 0.002 PHE A 56 TYR 0.017 0.001 TYR A 136 ARG 0.007 0.000 ARG J 126 Details of bonding type rmsd hydrogen bonds : bond 0.16683 ( 721) hydrogen bonds : angle 5.58241 ( 2103) metal coordination : bond 0.31614 ( 8) metal coordination : angle 3.90582 ( 6) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.31149 ( 4) covalent geometry : bond 0.00860 (16782) covalent geometry : angle 0.91032 (22879) Misc. bond : bond 0.32607 ( 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 : 1.864 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: 1.4542 time to fit residues: 347.0495 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 : 1.646 ------------------------------------------------------------------------------- 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 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 165 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3608 r_free = 0.3608 target = 0.141011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.104863 restraints weight = 19005.151| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.26 r_work: 0.2981 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.155 16801 Z= 0.135 Angle : 0.684 16.981 22889 Z= 0.306 Chirality : 0.046 0.211 2523 Planarity : 0.005 0.057 2711 Dihedral : 18.870 175.055 3298 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.69 % Allowed : 7.08 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1866 helix: 1.81 (0.18), residues: 921 sheet: -0.54 (0.34), residues: 201 loop : -1.72 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.006 0.001 HIS I 202 PHE 0.018 0.001 PHE A 131 TYR 0.011 0.001 TYR J 80 ARG 0.005 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.05984 ( 721) hydrogen bonds : angle 3.99404 ( 2103) metal coordination : bond 0.00981 ( 8) metal coordination : angle 4.55028 ( 6) SS BOND : bond 0.00263 ( 2) SS BOND : angle 1.06221 ( 4) covalent geometry : bond 0.00287 (16782) covalent geometry : angle 0.68041 (22879) Misc. bond : bond 0.08243 ( 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: 27 poor density : 182 time to evaluate : 1.719 Fit side-chains REVERT: A 13 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8373 (mt-10) REVERT: A 64 ASP cc_start: 0.8278 (m-30) cc_final: 0.7974 (m-30) REVERT: B 5 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7391 (tttm) REVERT: B 15 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7115 (mtp85) REVERT: B 119 LYS cc_start: 0.7497 (pmtt) cc_final: 0.6898 (tptm) REVERT: D 35 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7833 (mp) REVERT: E 27 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7911 (tptt) REVERT: F 8 ARG cc_start: 0.8217 (ttp-170) cc_final: 0.7988 (ttp80) REVERT: I 13 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7658 (mm-30) REVERT: K 184 ARG cc_start: 0.6961 (mpt180) cc_final: 0.6320 (ttm-80) REVERT: L 122 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8233 (ptpt) REVERT: O 3 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7972 (mt-10) outliers start: 27 outliers final: 13 residues processed: 194 average time/residue: 1.4843 time to fit residues: 316.7714 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 : 1.823 ------------------------------------------------------------------------------- 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 151 ILE 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 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 Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 167 optimal weight: 0.0570 chunk 79 optimal weight: 20.0000 chunk 21 optimal weight: 0.0370 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3583 r_free = 0.3583 target = 0.138890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103128 restraints weight = 18917.544| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.28 r_work: 0.2935 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 16801 Z= 0.141 Angle : 0.679 16.044 22889 Z= 0.301 Chirality : 0.046 0.263 2523 Planarity : 0.005 0.060 2711 Dihedral : 17.042 176.738 3272 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.44 % Allowed : 9.40 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 1866 helix: 1.97 (0.18), residues: 929 sheet: -0.30 (0.34), residues: 206 loop : -1.59 (0.20), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.009 0.001 HIS I 202 PHE 0.020 0.001 PHE A 131 TYR 0.013 0.001 TYR A 136 ARG 0.005 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.06944 ( 721) hydrogen bonds : angle 3.81409 ( 2103) metal coordination : bond 0.01393 ( 8) metal coordination : angle 4.23888 ( 6) SS BOND : bond 0.00410 ( 2) SS BOND : angle 1.31020 ( 4) covalent geometry : bond 0.00321 (16782) covalent geometry : angle 0.67523 (22879) Misc. bond : bond 0.07933 ( 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 193 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.835 Fit side-chains REVERT: A 13 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8442 (mt-10) REVERT: A 64 ASP cc_start: 0.8424 (m-30) cc_final: 0.8107 (m-30) REVERT: A 73 MET cc_start: 0.8808 (tpt) cc_final: 0.8513 (mmm) REVERT: B 5 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7420 (tttm) REVERT: B 6 LYS cc_start: 0.7888 (mmpt) cc_final: 0.7406 (mppt) REVERT: B 15 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7122 (mtp85) REVERT: B 119 LYS cc_start: 0.7520 (pmtt) cc_final: 0.7171 (mttp) REVERT: D 35 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7936 (mp) REVERT: E 27 LYS cc_start: 0.8188 (tppt) cc_final: 0.7974 (tptt) REVERT: I 13 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7728 (mm-30) REVERT: K 184 ARG cc_start: 0.6983 (mpt180) cc_final: 0.6752 (mpt180) REVERT: L 122 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8183 (ptpt) REVERT: M 29 ARG cc_start: 0.7814 (mpt180) cc_final: 0.7264 (mmm160) outliers start: 23 outliers final: 8 residues processed: 180 average time/residue: 1.4958 time to fit residues: 294.7551 Evaluate side-chains 175 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 91 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 M residue 26 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 83 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 54 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3584 r_free = 0.3584 target = 0.138985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.102622 restraints weight = 18894.646| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.25 r_work: 0.2917 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1527 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= 0.135 Angle : 0.656 16.407 22889 Z= 0.289 Chirality : 0.046 0.311 2523 Planarity : 0.005 0.058 2711 Dihedral : 16.072 178.017 3265 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.44 % Allowed : 9.52 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1866 helix: 2.15 (0.17), residues: 925 sheet: -0.30 (0.33), residues: 228 loop : -1.43 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.007 0.001 HIS I 202 PHE 0.014 0.001 PHE A 131 TYR 0.010 0.001 TYR A 136 ARG 0.005 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.06551 ( 721) hydrogen bonds : angle 3.70940 ( 2103) metal coordination : bond 0.00663 ( 8) metal coordination : angle 3.99004 ( 6) SS BOND : bond 0.00366 ( 2) SS BOND : angle 1.19118 ( 4) covalent geometry : bond 0.00307 (16782) covalent geometry : angle 0.65238 (22879) Misc. bond : bond 0.07483 ( 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 208 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.687 Fit side-chains REVERT: A 64 ASP cc_start: 0.8431 (m-30) cc_final: 0.8110 (m-30) REVERT: A 73 MET cc_start: 0.8805 (tpt) cc_final: 0.8537 (mmm) REVERT: B 5 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7494 (tttm) REVERT: B 6 LYS cc_start: 0.7970 (mmpt) cc_final: 0.7503 (mppt) REVERT: B 15 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7156 (mtp85) REVERT: B 119 LYS cc_start: 0.7490 (pmtt) cc_final: 0.7203 (mttt) REVERT: E 27 LYS cc_start: 0.8205 (tppt) cc_final: 0.7990 (tptt) REVERT: G 28 GLN cc_start: 0.8157 (tt0) cc_final: 0.7955 (mt0) REVERT: G 30 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6449 (mtt-85) REVERT: I 13 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7729 (mm-30) REVERT: K 184 ARG cc_start: 0.7059 (mpt180) cc_final: 0.6810 (mpt180) REVERT: L 122 LYS cc_start: 0.8455 (ptpt) cc_final: 0.8218 (ptpt) REVERT: M 29 ARG cc_start: 0.7793 (mpt180) cc_final: 0.7258 (mmm160) REVERT: O 3 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7700 (mt-10) outliers start: 39 outliers final: 16 residues processed: 186 average time/residue: 1.4442 time to fit residues: 294.7222 Evaluate side-chains 183 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR 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 G residue 1 MET Chi-restraints excluded: chain G residue 30 ARG 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 K residue 32 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 6 GLN ** 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 = 0.3529 r_free = 0.3529 target = 0.134355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.095421 restraints weight = 19332.148| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.52 r_work: 0.2830 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 16801 Z= 0.234 Angle : 0.818 16.956 22889 Z= 0.365 Chirality : 0.052 0.374 2523 Planarity : 0.006 0.062 2711 Dihedral : 16.594 178.593 3265 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.44 % Allowed : 10.71 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1866 helix: 1.69 (0.17), residues: 929 sheet: -0.16 (0.34), residues: 201 loop : -1.50 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 146 HIS 0.012 0.002 HIS I 202 PHE 0.020 0.002 PHE K 128 TYR 0.018 0.002 TYR A 136 ARG 0.005 0.001 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.09905 ( 721) hydrogen bonds : angle 3.97223 ( 2103) metal coordination : bond 0.01350 ( 8) metal coordination : angle 4.76167 ( 6) SS BOND : bond 0.00848 ( 2) SS BOND : angle 2.32790 ( 4) covalent geometry : bond 0.00589 (16782) covalent geometry : angle 0.81364 (22879) Misc. bond : bond 0.08189 ( 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: 39 poor density : 168 time to evaluate : 2.102 Fit side-chains REVERT: B 5 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7552 (tttp) REVERT: B 15 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7065 (mtp85) REVERT: B 119 LYS cc_start: 0.7602 (pmtt) cc_final: 0.7330 (mttp) REVERT: I 13 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7757 (mm-30) REVERT: J 119 LYS cc_start: 0.8753 (mptp) cc_final: 0.7420 (tttm) REVERT: K 184 ARG cc_start: 0.7019 (mpt180) cc_final: 0.6481 (ttm-80) outliers start: 39 outliers final: 21 residues processed: 187 average time/residue: 1.8068 time to fit residues: 370.7705 Evaluate side-chains 179 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 4.218 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 137 THR 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 G residue 1 MET Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 168 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 N residue 33 THR 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 16 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3560 r_free = 0.3560 target = 0.136957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.098959 restraints weight = 18990.631| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.35 r_work: 0.2865 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 16801 Z= 0.159 Angle : 0.704 17.136 22889 Z= 0.313 Chirality : 0.047 0.378 2523 Planarity : 0.005 0.058 2711 Dihedral : 15.968 179.616 3265 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.57 % Allowed : 11.53 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1866 helix: 1.90 (0.17), residues: 929 sheet: -0.27 (0.33), residues: 223 loop : -1.35 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 164 HIS 0.008 0.001 HIS I 202 PHE 0.014 0.002 PHE A 131 TYR 0.012 0.001 TYR A 136 ARG 0.005 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.07721 ( 721) hydrogen bonds : angle 3.81877 ( 2103) metal coordination : bond 0.00779 ( 8) metal coordination : angle 4.24185 ( 6) SS BOND : bond 0.00526 ( 2) SS BOND : angle 1.52479 ( 4) covalent geometry : bond 0.00371 (16782) covalent geometry : angle 0.70038 (22879) Misc. bond : bond 0.07104 ( 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 201 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.599 Fit side-chains REVERT: A 64 ASP cc_start: 0.8540 (m-30) cc_final: 0.8337 (m-30) REVERT: A 73 MET cc_start: 0.8845 (tpt) cc_final: 0.8582 (mmm) REVERT: B 5 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7571 (tttm) REVERT: B 15 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7060 (mtp85) REVERT: B 119 LYS cc_start: 0.7523 (pmtt) cc_final: 0.7312 (mttp) REVERT: C 110 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: D 140 ARG cc_start: 0.7661 (tmm-80) cc_final: 0.7298 (ttt90) REVERT: G 30 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.6954 (mtt-85) REVERT: I 13 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7765 (mm-30) REVERT: K 184 ARG cc_start: 0.7146 (mpt180) cc_final: 0.6573 (ttm-80) REVERT: M 29 ARG cc_start: 0.7847 (mpt180) cc_final: 0.7299 (mmm160) REVERT: O 3 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7856 (mt-10) outliers start: 41 outliers final: 24 residues processed: 180 average time/residue: 1.6264 time to fit residues: 319.2597 Evaluate side-chains 187 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR 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 C residue 110 GLN 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 1 MET 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 75 ILE Chi-restraints excluded: chain K residue 32 ASP 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 N residue 33 THR Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 85 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3573 r_free = 0.3573 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101195 restraints weight = 19117.083| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.38 r_work: 0.2891 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 16801 Z= 0.150 Angle : 0.680 16.747 22889 Z= 0.302 Chirality : 0.046 0.385 2523 Planarity : 0.005 0.057 2711 Dihedral : 15.435 177.578 3265 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.38 % Allowed : 12.22 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1866 helix: 2.05 (0.17), residues: 929 sheet: -0.13 (0.34), residues: 223 loop : -1.27 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.008 0.001 HIS I 202 PHE 0.013 0.001 PHE K 128 TYR 0.011 0.001 TYR A 136 ARG 0.005 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.07307 ( 721) hydrogen bonds : angle 3.72778 ( 2103) metal coordination : bond 0.00748 ( 8) metal coordination : angle 3.95694 ( 6) SS BOND : bond 0.00476 ( 2) SS BOND : angle 1.43090 ( 4) covalent geometry : bond 0.00351 (16782) covalent geometry : angle 0.67677 (22879) Misc. bond : bond 0.07416 ( 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 197 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 1.591 Fit side-chains REVERT: A 20 ASP cc_start: 0.8605 (t70) cc_final: 0.8360 (t0) REVERT: A 64 ASP cc_start: 0.8524 (m-30) cc_final: 0.8311 (m-30) REVERT: A 73 MET cc_start: 0.8843 (tpt) cc_final: 0.8592 (mmm) REVERT: A 131 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: B 5 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7657 (tttm) REVERT: B 6 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7622 (mppt) REVERT: B 15 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.6985 (mtp85) REVERT: B 119 LYS cc_start: 0.7519 (pmtt) cc_final: 0.7279 (mttt) REVERT: C 110 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: G 30 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6895 (mtt-85) REVERT: I 13 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7739 (mm-30) REVERT: K 184 ARG cc_start: 0.7173 (mpt180) cc_final: 0.6528 (ttm-80) REVERT: L 122 LYS cc_start: 0.8470 (ptpt) cc_final: 0.8237 (ptpt) REVERT: M 29 ARG cc_start: 0.7826 (mpt180) cc_final: 0.7291 (mmm160) outliers start: 38 outliers final: 25 residues processed: 182 average time/residue: 1.7027 time to fit residues: 339.5955 Evaluate side-chains 185 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 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 110 GLN 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 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 168 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 32 ASP 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 N residue 33 THR Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 28 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 123 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 132 optimal weight: 0.0020 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3557 r_free = 0.3557 target = 0.136615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099895 restraints weight = 18960.346| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.36 r_work: 0.2871 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 0.162 16801 Z= 0.171 Angle : 0.715 17.019 22889 Z= 0.319 Chirality : 0.048 0.361 2523 Planarity : 0.005 0.058 2711 Dihedral : 15.454 176.513 3265 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.38 % Allowed : 12.34 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 1866 helix: 1.95 (0.17), residues: 929 sheet: -0.10 (0.34), residues: 217 loop : -1.31 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.009 0.001 HIS I 202 PHE 0.015 0.002 PHE K 128 TYR 0.013 0.001 TYR A 136 ARG 0.004 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.08177 ( 721) hydrogen bonds : angle 3.79413 ( 2103) metal coordination : bond 0.00930 ( 8) metal coordination : angle 4.16009 ( 6) SS BOND : bond 0.00593 ( 2) SS BOND : angle 1.70352 ( 4) covalent geometry : bond 0.00409 (16782) covalent geometry : angle 0.71154 (22879) Misc. bond : bond 0.07558 ( 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 200 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 2.077 Fit side-chains REVERT: A 73 MET cc_start: 0.8843 (tpt) cc_final: 0.8592 (mmm) REVERT: A 131 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: B 5 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7635 (tttm) REVERT: B 6 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7655 (mppt) REVERT: B 15 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.6986 (mtp85) REVERT: B 119 LYS cc_start: 0.7546 (pmtt) cc_final: 0.7307 (mttt) REVERT: C 110 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7839 (mm-40) REVERT: I 13 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7766 (mm-30) REVERT: J 119 LYS cc_start: 0.8768 (mptp) cc_final: 0.7510 (tttm) REVERT: K 184 ARG cc_start: 0.7206 (mpt180) cc_final: 0.6589 (ttm-80) REVERT: L 122 LYS cc_start: 0.8507 (ptpt) cc_final: 0.8269 (ptpt) REVERT: M 29 ARG cc_start: 0.7849 (mpt180) cc_final: 0.7368 (mmm160) outliers start: 38 outliers final: 24 residues processed: 182 average time/residue: 1.8094 time to fit residues: 359.8527 Evaluate side-chains 188 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 110 GLN 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 1 MET Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 1 MET 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 168 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 122 LYS Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3595 r_free = 0.3595 target = 0.139818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103485 restraints weight = 18996.163| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.26 r_work: 0.2955 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 16801 Z= 0.129 Angle : 0.634 16.588 22889 Z= 0.282 Chirality : 0.044 0.281 2523 Planarity : 0.005 0.058 2711 Dihedral : 14.887 173.894 3265 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.82 % Allowed : 12.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1866 helix: 2.30 (0.17), residues: 925 sheet: 0.12 (0.35), residues: 208 loop : -1.20 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.006 0.001 HIS I 202 PHE 0.011 0.001 PHE A 198 TYR 0.008 0.001 TYR J 80 ARG 0.004 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.06287 ( 721) hydrogen bonds : angle 3.63389 ( 2103) metal coordination : bond 0.00552 ( 8) metal coordination : angle 3.92889 ( 6) SS BOND : bond 0.00359 ( 2) SS BOND : angle 1.12001 ( 4) covalent geometry : bond 0.00293 (16782) covalent geometry : angle 0.63060 (22879) Misc. bond : bond 0.07184 ( 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 194 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 2.026 Fit side-chains REVERT: A 20 ASP cc_start: 0.8574 (t70) cc_final: 0.8324 (t0) REVERT: A 73 MET cc_start: 0.8795 (tpt) cc_final: 0.8543 (mmm) REVERT: A 131 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: B 5 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7598 (tttm) REVERT: B 6 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7472 (mppt) REVERT: B 15 ARG cc_start: 0.7453 (mtm-85) cc_final: 0.6922 (mtp85) REVERT: B 119 LYS cc_start: 0.7446 (pmtt) cc_final: 0.7223 (mttt) REVERT: C 65 LYS cc_start: 0.7379 (mttt) cc_final: 0.7026 (mmtp) REVERT: I 13 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7693 (mm-30) REVERT: I 131 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.6993 (t80) REVERT: J 119 LYS cc_start: 0.8776 (mptp) cc_final: 0.7482 (tttm) REVERT: K 184 ARG cc_start: 0.7230 (mpt180) cc_final: 0.6551 (ttm-80) REVERT: L 122 LYS cc_start: 0.8435 (ptpt) cc_final: 0.8217 (ptpt) REVERT: M 29 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7280 (mmm160) REVERT: P 1 MET cc_start: 0.5579 (pmm) cc_final: 0.5323 (ptt) outliers start: 29 outliers final: 21 residues processed: 183 average time/residue: 1.6481 time to fit residues: 331.0382 Evaluate side-chains 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.809 ------------------------------------------------------------------------------- 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 A residue 148 VAL Chi-restraints excluded: chain A residue 179 THR 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 E residue 1 MET Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 1 MET 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 168 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 122 LYS Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain N residue 33 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 0.0030 chunk 116 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3611 r_free = 0.3611 target = 0.141254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105260 restraints weight = 19013.302| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.28 r_work: 0.2978 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.178 16801 Z= 0.120 Angle : 0.608 16.268 22889 Z= 0.271 Chirality : 0.043 0.203 2523 Planarity : 0.005 0.058 2711 Dihedral : 14.375 170.519 3265 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.50 % Allowed : 13.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1866 helix: 2.47 (0.17), residues: 925 sheet: 0.20 (0.36), residues: 208 loop : -1.09 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 118 HIS 0.005 0.001 HIS I 202 PHE 0.013 0.001 PHE I 198 TYR 0.008 0.001 TYR J 80 ARG 0.006 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.05787 ( 721) hydrogen bonds : angle 3.52980 ( 2103) metal coordination : bond 0.00624 ( 8) metal coordination : angle 3.82713 ( 6) SS BOND : bond 0.00286 ( 2) SS BOND : angle 1.01252 ( 4) covalent geometry : bond 0.00268 (16782) covalent geometry : angle 0.60480 (22879) Misc. bond : bond 0.07166 ( 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 195 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.867 Fit side-chains REVERT: A 20 ASP cc_start: 0.8535 (t70) cc_final: 0.8279 (t0) REVERT: A 73 MET cc_start: 0.8768 (tpt) cc_final: 0.8515 (mmm) REVERT: A 131 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: B 5 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7595 (tttm) REVERT: B 6 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7459 (mppt) REVERT: B 15 ARG cc_start: 0.7455 (mtm-85) cc_final: 0.6982 (mtm110) REVERT: B 119 LYS cc_start: 0.7413 (pmtt) cc_final: 0.7195 (mttt) REVERT: C 110 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7801 (mm-40) REVERT: I 13 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7641 (mm-30) REVERT: I 131 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.7069 (t80) REVERT: J 119 LYS cc_start: 0.8751 (mptp) cc_final: 0.7436 (tttm) REVERT: K 184 ARG cc_start: 0.7244 (mpt180) cc_final: 0.6555 (ttm-80) REVERT: L 122 LYS cc_start: 0.8403 (ptpt) cc_final: 0.8199 (ptpt) REVERT: M 29 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7247 (mmm160) REVERT: P 1 MET cc_start: 0.5578 (pmm) cc_final: 0.5365 (ptt) outliers start: 24 outliers final: 16 residues processed: 186 average time/residue: 1.4629 time to fit residues: 298.9226 Evaluate side-chains 186 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 1.615 ------------------------------------------------------------------------------- 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 A residue 179 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain C residue 110 GLN 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 G residue 1 MET 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 K residue 122 LYS Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 29 ARG Chi-restraints excluded: chain N residue 33 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 110 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 131 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3610 r_free = 0.3610 target = 0.141216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104829 restraints weight = 18917.968| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.25 r_work: 0.2980 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1936 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= 0.121 Angle : 0.606 16.470 22889 Z= 0.271 Chirality : 0.043 0.169 2523 Planarity : 0.005 0.058 2711 Dihedral : 14.216 168.338 3263 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.63 % Allowed : 13.60 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1866 helix: 2.50 (0.17), residues: 925 sheet: 0.20 (0.36), residues: 209 loop : -1.01 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.005 0.001 HIS I 202 PHE 0.016 0.001 PHE A 198 TYR 0.008 0.001 TYR J 80 ARG 0.006 0.000 ARG O 30 Details of bonding type rmsd hydrogen bonds : bond 0.05856 ( 721) hydrogen bonds : angle 3.51958 ( 2103) metal coordination : bond 0.00609 ( 8) metal coordination : angle 3.75924 ( 6) SS BOND : bond 0.00312 ( 2) SS BOND : angle 1.04910 ( 4) covalent geometry : bond 0.00269 (16782) covalent geometry : angle 0.60333 (22879) Misc. bond : bond 0.07382 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13396.97 seconds wall clock time: 231 minutes 3.66 seconds (13863.66 seconds total)