Starting phenix.real_space_refine on Thu Feb 5 11:09:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgg_55898/02_2026/9tgg_55898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgg_55898/02_2026/9tgg_55898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tgg_55898/02_2026/9tgg_55898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgg_55898/02_2026/9tgg_55898.map" model { file = "/net/cci-nas-00/data/ceres_data/9tgg_55898/02_2026/9tgg_55898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgg_55898/02_2026/9tgg_55898.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 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 Cu 1 5.60 5 Mg 2 5.21 5 S 75 5.16 5 C 11179 2.51 5 N 2561 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16731 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1225 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 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: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1259 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 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: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1259 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "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: "Q" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 93} Chain: "A" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 372 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'PL9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 362 Unusual residues: {'HEC': 1, 'HEM': 2, 'PL9': 3, 'UMQ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 120 Unusual residues: {'CLA': 1, 'PL9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 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} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5835 SG CYS D 107 100.456 53.122 49.719 1.00 65.18 S ATOM 5971 SG CYS D 125 97.978 53.297 46.731 1.00 65.20 S ATOM 13204 SG CYS L 107 41.357 64.336 78.236 1.00 74.27 S ATOM 13340 SG CYS L 125 43.323 62.430 80.967 1.00 67.21 S ATOM 15368 SG CYS Q 84 44.908 29.866 107.358 1.00 27.08 S Time building chain proxies: 3.37, per 1000 atoms: 0.20 Number of scatterers: 16731 At special positions: 0 Unit cell: (129.86, 135.02, 132.44, 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) Cu 1 28.99 Fe 12 26.01 S 75 16.00 Mg 2 11.99 O 2901 8.00 N 2561 7.00 C 11179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 730.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 128 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 109 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 107 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 125 " pdb=" FES L 201 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 128 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 109 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 107 " Number of angles added : 6 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 18 sheets defined 49.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 4.044A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.565A pdb=" N ALA A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.513A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.686A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 removed outlier: 3.697A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.614A pdb=" N ILE A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.565A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.666A pdb=" N LEU A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 210 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.682A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.732A pdb=" N TYR B 26 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR B 27 " --> pdb=" O HIS B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 39 through 58 removed outlier: 3.617A 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 removed outlier: 3.676A pdb=" N ILE B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 109 removed outlier: 4.028A 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: 4.678A 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 85 through 89 removed outlier: 3.931A pdb=" N ILE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.613A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 33 removed outlier: 4.117A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix removed outlier: 3.505A pdb=" N MET D 33 " --> pdb=" O PRO D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 40 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.571A pdb=" N ILE E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.513A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 31 removed outlier: 3.671A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 27 removed outlier: 3.531A pdb=" N LEU H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA H 7 " --> pdb=" O ILE H 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 22 " --> pdb=" O SER H 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 13 removed outlier: 3.984A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 31 through 34 Processing helix chain 'I' and resid 35 through 55 removed outlier: 3.563A pdb=" N THR I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 78 through 107 removed outlier: 3.600A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.707A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.689A pdb=" N ILE I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 157 removed outlier: 3.618A pdb=" N ASP I 156 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA I 157 " --> pdb=" O VAL I 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 153 through 157' Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.786A pdb=" N LEU I 165 " --> pdb=" O ILE I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 189 removed outlier: 3.671A pdb=" N LEU I 180 " --> pdb=" O GLY I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 210 Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.839A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 27 removed outlier: 3.748A pdb=" N TYR J 26 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR J 27 " --> pdb=" O HIS J 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 23 through 27' Processing helix chain 'J' and resid 39 through 58 removed outlier: 3.565A 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: 3.991A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.866A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 115 removed outlier: 3.542A pdb=" N GLU J 115 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.604A pdb=" N SER J 154 " --> pdb=" O ILE J 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 19 through 24 removed outlier: 3.824A pdb=" N ASN K 23 " --> pdb=" O VAL K 20 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS K 24 " --> pdb=" O CYS K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.531A pdb=" N ILE K 89 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.787A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.587A pdb=" N ILE K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 33 removed outlier: 3.620A pdb=" N LEU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix Processing helix chain 'L' and resid 34 through 40 Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.506A pdb=" N HIS L 72 " --> pdb=" O TRP L 68 " (cutoff:3.500A) 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: 3.563A pdb=" N THR N 17 " --> pdb=" O MET N 13 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 30 removed outlier: 3.716A 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 27 removed outlier: 3.505A pdb=" N VAL P 22 " --> pdb=" O SER P 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 46 removed outlier: 4.184A pdb=" N ILE Q 46 " --> pdb=" O GLU Q 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 43 through 46' Processing helix chain 'Q' and resid 51 through 56 removed outlier: 3.950A pdb=" N ILE Q 55 " --> pdb=" O ASP Q 51 " (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: 3.928A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.607A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 73 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.668A pdb=" N GLY C 67 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 177 through 184 removed outlier: 5.386A pdb=" N VAL C 179 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA C 195 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.562A pdb=" N THR D 53 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS D 152 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR D 100 " --> pdb=" O CYS D 152 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL D 154 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 11.659A pdb=" N LEU D 98 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.884A 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: 3.817A 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: 3.501A pdb=" N TYR K 149 " --> pdb=" O ILE K 76 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA K 73 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN K 103 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 38 through 39 removed outlier: 3.501A pdb=" N TYR K 149 " --> pdb=" O ILE K 76 " (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: 3.586A pdb=" N TYR K 190 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY K 189 " --> pdb=" O ARG K 184 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG K 184 " --> pdb=" O GLY K 189 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU K 191 " --> pdb=" O ILE K 182 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE K 182 " --> pdb=" O GLU K 191 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN K 193 " --> pdb=" O LYS K 180 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY K 177 " --> pdb=" O ILE K 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.402A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.549A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 14 through 15 Processing sheet with id=AB9, first strand: chain 'Q' and resid 18 through 21 790 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.80 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: 6541 1.39 - 1.59: 10481 1.59 - 1.79: 54 1.79 - 2.00: 67 2.00 - 2.20: 48 Bond restraints: 17191 Sorted by residual: bond pdb=" N ALA Q 52 " pdb=" CA ALA Q 52 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.30e-02 5.92e+03 8.65e+00 bond pdb=" N ASP Q 51 " pdb=" CA ASP Q 51 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.23e-02 6.61e+03 8.43e+00 bond pdb=" N GLY J 2 " pdb=" CA GLY J 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.26e+00 bond pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.04e+00 bond pdb=" CA GLY Q 94 " pdb=" C GLY Q 94 " ideal model delta sigma weight residual 1.513 1.539 -0.026 1.09e-02 8.42e+03 5.81e+00 ... (remaining 17186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 23113 2.63 - 5.26: 350 5.26 - 7.89: 18 7.89 - 10.52: 4 10.52 - 13.15: 2 Bond angle restraints: 23487 Sorted by residual: angle pdb=" O GLY Q 94 " pdb=" C GLY Q 94 " pdb=" N LYS Q 95 " ideal model delta sigma weight residual 123.45 128.62 -5.17 1.06e+00 8.90e-01 2.37e+01 angle pdb=" N GLU Q 59 " pdb=" CA GLU Q 59 " pdb=" C GLU Q 59 " ideal model delta sigma weight residual 111.71 117.29 -5.58 1.15e+00 7.56e-01 2.35e+01 angle pdb=" CA GLY Q 67 " pdb=" C GLY Q 67 " pdb=" O GLY Q 67 " ideal model delta sigma weight residual 119.07 113.78 5.29 1.12e+00 7.97e-01 2.23e+01 angle pdb=" C PHE Q 35 " pdb=" CA PHE Q 35 " pdb=" CB PHE Q 35 " ideal model delta sigma weight residual 110.31 119.95 -9.64 2.06e+00 2.36e-01 2.19e+01 angle pdb=" CA GLY Q 8 " pdb=" C GLY Q 8 " pdb=" N ASP Q 9 " ideal model delta sigma weight residual 117.79 112.71 5.08 1.12e+00 7.97e-01 2.06e+01 ... (remaining 23482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9066 17.99 - 35.98: 823 35.98 - 53.97: 193 53.97 - 71.96: 56 71.96 - 89.96: 20 Dihedral angle restraints: 10158 sinusoidal: 4459 harmonic: 5699 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 -120.00 -169.95 49.95 2 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" C2C HEC I 304 " pdb=" C3C HEC I 304 " pdb=" CAC HEC I 304 " pdb=" CBC HEC I 304 " ideal model delta sinusoidal sigma weight residual -120.00 -169.49 49.49 2 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS L 112 " pdb=" SG CYS L 112 " pdb=" SG CYS L 127 " pdb=" CB CYS L 127 " ideal model delta sinusoidal sigma weight residual -86.00 -128.99 42.99 1 1.00e+01 1.00e-02 2.58e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2121 0.058 - 0.115: 391 0.115 - 0.173: 59 0.173 - 0.230: 12 0.230 - 0.288: 5 Chirality restraints: 2588 Sorted by residual: chirality pdb=" CA ASP Q 51 " pdb=" N ASP Q 51 " pdb=" C ASP Q 51 " pdb=" CB ASP Q 51 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA GLU Q 59 " pdb=" N GLU Q 59 " pdb=" C GLU Q 59 " pdb=" CB GLU Q 59 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA PRO Q 86 " pdb=" N PRO Q 86 " pdb=" C PRO Q 86 " pdb=" CB PRO Q 86 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2585 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER Q 85 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C SER Q 85 " 0.058 2.00e-02 2.50e+03 pdb=" O SER Q 85 " -0.021 2.00e-02 2.50e+03 pdb=" N PRO Q 86 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 43 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLU Q 43 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU Q 43 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP Q 44 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 10 " 0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C GLY Q 10 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY Q 10 " 0.018 2.00e-02 2.50e+03 pdb=" N SER Q 11 " 0.017 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 44 2.55 - 3.14: 12679 3.14 - 3.73: 23207 3.73 - 4.31: 33216 4.31 - 4.90: 55471 Nonbonded interactions: 124617 Sorted by model distance: nonbonded pdb=" ND1 HIS Q 37 " pdb="CU CU Q 200 " model vdw 1.964 2.320 nonbonded pdb=" SG CYS Q 84 " pdb="CU CU Q 200 " model vdw 2.149 2.600 nonbonded pdb=" O GLY K 98 " pdb=" OD1 ASN K 99 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR I 5 " pdb=" OE1 GLN I 15 " model vdw 2.208 3.040 nonbonded pdb=" NE2 HIS I 86 " pdb="FE HEM I 302 " model vdw 2.357 3.080 ... (remaining 124612 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 305 or resid 308)) selection = (chain 'I' and (resid 2 through 215 or resid 302 or resid 305 or resid 308)) } ncs_group { reference = (chain 'B' and resid 2 through 160) selection = (chain 'J' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) } ncs_group { reference = chain 'C' selection = (chain 'K' and resid 1 through 301) } ncs_group { reference = (chain 'D' and resid 8 through 201) selection = chain 'L' } ncs_group { reference = (chain 'E' and resid 1 through 31) selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' 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)) or resid 101)) } 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 17211 Z= 0.228 Angle : 0.730 15.466 23497 Z= 0.371 Chirality : 0.048 0.288 2588 Planarity : 0.005 0.051 2839 Dihedral : 15.108 89.955 6500 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 0.30 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1963 helix: 1.85 (0.18), residues: 880 sheet: -0.12 (0.32), residues: 244 loop : -1.09 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 89 TYR 0.015 0.001 TYR I 136 PHE 0.026 0.001 PHE Q 35 TRP 0.007 0.001 TRP H 24 HIS 0.008 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00477 (17191) covalent geometry : angle 0.70574 (23487) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.27652 ( 4) hydrogen bonds : bond 0.30082 ( 773) hydrogen bonds : angle 6.58525 ( 2259) metal coordination : bond 0.05176 ( 8) metal coordination : angle 11.57497 ( 6) Misc. bond : bond 0.07387 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 335 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7574 (m-30) cc_final: 0.7310 (m-30) REVERT: A 73 MET cc_start: 0.8851 (tpt) cc_final: 0.8605 (mmp) REVERT: C 11 ASN cc_start: 0.8065 (t0) cc_final: 0.7424 (t0) REVERT: C 34 GLU cc_start: 0.7897 (tt0) cc_final: 0.7317 (mt-10) REVERT: D 9 VAL cc_start: 0.8571 (m) cc_final: 0.8293 (p) REVERT: F 5 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7914 (mm-30) REVERT: K 109 LYS cc_start: 0.7442 (mttm) cc_final: 0.7075 (mmtt) REVERT: P 1 MET cc_start: 0.6854 (pmm) cc_final: 0.6626 (ptp) outliers start: 4 outliers final: 3 residues processed: 338 average time/residue: 0.0835 time to fit residues: 48.2317 Evaluate side-chains 296 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 293 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 64 ASN Chi-restraints excluded: chain Q residue 92 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN I 77 ASN I 177 GLN K 23 ASN K 153 ASN L 72 HIS L 131 GLN Q 64 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.182888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.135788 restraints weight = 17583.289| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.86 r_work: 0.2831 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 17211 Z= 0.190 Angle : 0.659 11.747 23497 Z= 0.315 Chirality : 0.047 0.161 2588 Planarity : 0.005 0.061 2839 Dihedral : 12.943 85.177 2941 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.85 % Allowed : 8.24 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.19), residues: 1963 helix: 2.26 (0.17), residues: 910 sheet: 0.21 (0.33), residues: 228 loop : -1.11 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 11 TYR 0.015 0.001 TYR I 136 PHE 0.017 0.001 PHE K 128 TRP 0.011 0.001 TRP D 164 HIS 0.009 0.002 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00458 (17191) covalent geometry : angle 0.64889 (23487) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.54454 ( 4) hydrogen bonds : bond 0.09433 ( 773) hydrogen bonds : angle 4.53203 ( 2259) metal coordination : bond 0.01396 ( 8) metal coordination : angle 7.13745 ( 6) Misc. bond : bond 0.08363 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 291 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9141 (mp) cc_final: 0.8917 (mm) REVERT: A 150 ILE cc_start: 0.8739 (mm) cc_final: 0.8482 (mt) REVERT: B 101 MET cc_start: 0.7334 (ptp) cc_final: 0.7087 (ptp) REVERT: C 34 GLU cc_start: 0.7733 (tt0) cc_final: 0.7468 (tt0) REVERT: D 9 VAL cc_start: 0.8561 (m) cc_final: 0.8273 (p) REVERT: I 150 ILE cc_start: 0.8826 (mt) cc_final: 0.8477 (mp) REVERT: J 20 LYS cc_start: 0.7894 (mtpp) cc_final: 0.7692 (mtmt) REVERT: K 83 LEU cc_start: 0.7681 (tt) cc_final: 0.7479 (tt) REVERT: K 109 LYS cc_start: 0.7550 (mttm) cc_final: 0.7106 (mmtt) REVERT: N 30 ILE cc_start: 0.7956 (mt) cc_final: 0.7638 (mt) REVERT: P 1 MET cc_start: 0.6701 (pmm) cc_final: 0.6307 (ptp) outliers start: 31 outliers final: 19 residues processed: 301 average time/residue: 0.0937 time to fit residues: 47.4185 Evaluate side-chains 292 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 158 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 178 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.185248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.137165 restraints weight = 17952.722| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.79 r_work: 0.2882 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 17211 Z= 0.140 Angle : 0.579 10.372 23497 Z= 0.272 Chirality : 0.044 0.155 2588 Planarity : 0.005 0.064 2839 Dihedral : 12.396 85.179 2933 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.37 % Allowed : 11.70 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.19), residues: 1963 helix: 2.41 (0.17), residues: 910 sheet: 0.41 (0.34), residues: 218 loop : -0.97 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 11 TYR 0.011 0.001 TYR B 80 PHE 0.010 0.001 PHE K 128 TRP 0.010 0.001 TRP D 164 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00336 (17191) covalent geometry : angle 0.57012 (23487) SS BOND : bond 0.00169 ( 2) SS BOND : angle 1.16113 ( 4) hydrogen bonds : bond 0.07169 ( 773) hydrogen bonds : angle 4.05384 ( 2259) metal coordination : bond 0.00886 ( 8) metal coordination : angle 6.36205 ( 6) Misc. bond : bond 0.05341 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 283 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7742 (m-30) cc_final: 0.7505 (m-30) REVERT: A 150 ILE cc_start: 0.8685 (mm) cc_final: 0.8463 (mt) REVERT: C 34 GLU cc_start: 0.7734 (tt0) cc_final: 0.7497 (tt0) REVERT: F 23 ILE cc_start: 0.8444 (mm) cc_final: 0.8211 (mm) REVERT: I 150 ILE cc_start: 0.8817 (mt) cc_final: 0.8472 (mp) REVERT: I 167 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7658 (mm-30) REVERT: J 20 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7724 (mtmt) REVERT: K 109 LYS cc_start: 0.7522 (mttm) cc_final: 0.7069 (mmtt) REVERT: K 111 ASN cc_start: 0.8620 (p0) cc_final: 0.8394 (p0) REVERT: L 97 THR cc_start: 0.7943 (m) cc_final: 0.7526 (t) REVERT: N 30 ILE cc_start: 0.7809 (mt) cc_final: 0.7540 (mt) REVERT: P 1 MET cc_start: 0.6429 (pmm) cc_final: 0.5990 (ptp) outliers start: 23 outliers final: 14 residues processed: 291 average time/residue: 0.0899 time to fit residues: 43.8667 Evaluate side-chains 284 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 270 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 21 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 157 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN G 28 GLN L 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.185163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.137858 restraints weight = 17785.960| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.68 r_work: 0.2886 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 17211 Z= 0.148 Angle : 0.577 10.836 23497 Z= 0.269 Chirality : 0.044 0.155 2588 Planarity : 0.005 0.065 2839 Dihedral : 12.118 88.985 2933 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 12.48 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.19), residues: 1963 helix: 2.41 (0.17), residues: 914 sheet: 0.56 (0.34), residues: 218 loop : -0.93 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.010 0.001 TYR B 80 PHE 0.012 0.001 PHE K 128 TRP 0.010 0.001 TRP J 142 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00368 (17191) covalent geometry : angle 0.56886 (23487) SS BOND : bond 0.00185 ( 2) SS BOND : angle 1.30134 ( 4) hydrogen bonds : bond 0.06902 ( 773) hydrogen bonds : angle 3.87039 ( 2259) metal coordination : bond 0.00933 ( 8) metal coordination : angle 6.16417 ( 6) Misc. bond : bond 0.06657 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7766 (m-30) cc_final: 0.7527 (m-30) REVERT: A 150 ILE cc_start: 0.8692 (mm) cc_final: 0.8490 (mt) REVERT: C 34 GLU cc_start: 0.7720 (tt0) cc_final: 0.7477 (tt0) REVERT: F 23 ILE cc_start: 0.8479 (mm) cc_final: 0.8266 (mm) REVERT: I 167 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7737 (mm-30) REVERT: J 20 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7751 (mtmt) REVERT: K 109 LYS cc_start: 0.7545 (mttm) cc_final: 0.7055 (mmtt) REVERT: K 111 ASN cc_start: 0.8642 (p0) cc_final: 0.8416 (p0) REVERT: K 276 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7171 (pt0) REVERT: L 97 THR cc_start: 0.7934 (m) cc_final: 0.7523 (t) REVERT: N 30 ILE cc_start: 0.7760 (mt) cc_final: 0.7398 (mt) REVERT: P 1 MET cc_start: 0.6012 (pmm) cc_final: 0.5550 (ptp) outliers start: 33 outliers final: 19 residues processed: 297 average time/residue: 0.0926 time to fit residues: 46.2524 Evaluate side-chains 295 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 28 GLN Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 280 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 142 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 28 optimal weight: 0.0040 chunk 85 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 HIS ** Q 31 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 = 0.3962 r_free = 0.3962 target = 0.186728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139658 restraints weight = 17764.572| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.61 r_work: 0.2919 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.126 17211 Z= 0.120 Angle : 0.548 9.948 23497 Z= 0.255 Chirality : 0.043 0.152 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.869 86.564 2933 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.61 % Allowed : 13.91 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 1963 helix: 2.57 (0.17), residues: 910 sheet: 0.72 (0.34), residues: 219 loop : -0.93 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 137 TYR 0.009 0.001 TYR B 80 PHE 0.010 0.001 PHE I 52 TRP 0.010 0.001 TRP J 142 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00286 (17191) covalent geometry : angle 0.53960 (23487) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.03127 ( 4) hydrogen bonds : bond 0.06049 ( 773) hydrogen bonds : angle 3.75606 ( 2259) metal coordination : bond 0.00732 ( 8) metal coordination : angle 5.83161 ( 6) Misc. bond : bond 0.05477 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 282 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9144 (mp) cc_final: 0.8937 (mm) REVERT: A 64 ASP cc_start: 0.7712 (m-30) cc_final: 0.7509 (m-30) REVERT: A 150 ILE cc_start: 0.8655 (mm) cc_final: 0.8432 (mt) REVERT: A 207 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7974 (ttm-80) REVERT: C 34 GLU cc_start: 0.7702 (tt0) cc_final: 0.7482 (tt0) REVERT: F 23 ILE cc_start: 0.8432 (mm) cc_final: 0.8215 (mm) REVERT: I 167 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7760 (mm-30) REVERT: J 20 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7742 (mtmt) REVERT: K 109 LYS cc_start: 0.7540 (mttm) cc_final: 0.7041 (mmtt) REVERT: K 111 ASN cc_start: 0.8616 (p0) cc_final: 0.8404 (p0) REVERT: L 97 THR cc_start: 0.7943 (m) cc_final: 0.7551 (t) REVERT: L 127 CYS cc_start: 0.7881 (m) cc_final: 0.7577 (m) REVERT: N 30 ILE cc_start: 0.7718 (mt) cc_final: 0.7394 (mt) outliers start: 27 outliers final: 20 residues processed: 295 average time/residue: 0.0923 time to fit residues: 45.8046 Evaluate side-chains 300 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 280 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 65 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 6.9990 chunk 22 optimal weight: 0.0040 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 123 optimal weight: 0.0070 chunk 153 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN C 274 GLN L 117 ASN ** Q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.186308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139067 restraints weight = 17694.805| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.67 r_work: 0.2908 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 17211 Z= 0.128 Angle : 0.550 10.230 23497 Z= 0.255 Chirality : 0.043 0.153 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.698 87.022 2933 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.79 % Allowed : 14.45 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1963 helix: 2.60 (0.17), residues: 910 sheet: 0.73 (0.34), residues: 215 loop : -0.92 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 29 TYR 0.010 0.001 TYR B 80 PHE 0.013 0.001 PHE D 116 TRP 0.010 0.001 TRP J 142 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00313 (17191) covalent geometry : angle 0.54207 (23487) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.06398 ( 4) hydrogen bonds : bond 0.06061 ( 773) hydrogen bonds : angle 3.69660 ( 2259) metal coordination : bond 0.00791 ( 8) metal coordination : angle 5.65215 ( 6) Misc. bond : bond 0.05571 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 269 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9119 (mp) cc_final: 0.8906 (mm) REVERT: A 150 ILE cc_start: 0.8633 (mm) cc_final: 0.8411 (mt) REVERT: A 207 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7963 (ttm-80) REVERT: B 5 LYS cc_start: 0.7928 (tttt) cc_final: 0.7705 (tttm) REVERT: C 34 GLU cc_start: 0.7661 (tt0) cc_final: 0.7458 (tt0) REVERT: D 134 ASN cc_start: 0.7866 (p0) cc_final: 0.7445 (t0) REVERT: I 167 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7687 (mm-30) REVERT: J 20 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7750 (mtmt) REVERT: K 55 MET cc_start: 0.6907 (mmt) cc_final: 0.6690 (mmt) REVERT: K 109 LYS cc_start: 0.7570 (mttm) cc_final: 0.7035 (mmtt) REVERT: K 111 ASN cc_start: 0.8618 (p0) cc_final: 0.8406 (p0) REVERT: L 97 THR cc_start: 0.7897 (m) cc_final: 0.7512 (t) REVERT: L 127 CYS cc_start: 0.7808 (m) cc_final: 0.7496 (m) REVERT: N 30 ILE cc_start: 0.7674 (mt) cc_final: 0.7343 (mt) outliers start: 30 outliers final: 24 residues processed: 283 average time/residue: 0.0849 time to fit residues: 40.3409 Evaluate side-chains 289 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 100 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 112 optimal weight: 0.0050 chunk 172 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 HIS ** Q 31 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 = 0.3947 r_free = 0.3947 target = 0.185206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.137667 restraints weight = 17607.796| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.48 r_work: 0.2897 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 17211 Z= 0.154 Angle : 0.577 11.474 23497 Z= 0.266 Chirality : 0.044 0.155 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.663 88.032 2933 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.09 % Allowed : 14.93 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1963 helix: 2.55 (0.17), residues: 906 sheet: 0.76 (0.34), residues: 225 loop : -0.95 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 29 TYR 0.011 0.001 TYR B 80 PHE 0.014 0.001 PHE K 128 TRP 0.011 0.001 TRP J 142 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00389 (17191) covalent geometry : angle 0.56889 (23487) SS BOND : bond 0.00221 ( 2) SS BOND : angle 1.28769 ( 4) hydrogen bonds : bond 0.06750 ( 773) hydrogen bonds : angle 3.72044 ( 2259) metal coordination : bond 0.00973 ( 8) metal coordination : angle 5.91029 ( 6) Misc. bond : bond 0.06379 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 269 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8703 (mm) cc_final: 0.8440 (mt) REVERT: A 207 ARG cc_start: 0.8289 (ttt90) cc_final: 0.8014 (ttm-80) REVERT: B 5 LYS cc_start: 0.7900 (tttt) cc_final: 0.7673 (tttm) REVERT: B 145 ILE cc_start: 0.8392 (mm) cc_final: 0.8056 (mm) REVERT: D 134 ASN cc_start: 0.7840 (p0) cc_final: 0.7493 (t0) REVERT: F 30 ILE cc_start: 0.7705 (mp) cc_final: 0.7489 (mp) REVERT: I 167 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7745 (mm-30) REVERT: J 20 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7736 (mtmt) REVERT: K 55 MET cc_start: 0.6914 (mmt) cc_final: 0.6696 (mmt) REVERT: K 109 LYS cc_start: 0.7531 (mttm) cc_final: 0.6994 (mmmt) REVERT: K 111 ASN cc_start: 0.8637 (p0) cc_final: 0.8410 (p0) REVERT: L 127 CYS cc_start: 0.7734 (m) cc_final: 0.7427 (m) REVERT: N 30 ILE cc_start: 0.7720 (mt) cc_final: 0.7382 (mt) outliers start: 35 outliers final: 28 residues processed: 287 average time/residue: 0.0912 time to fit residues: 43.5964 Evaluate side-chains 298 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 97 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 26 optimal weight: 0.4980 chunk 189 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 158 GLN L 72 HIS L 131 GLN ** Q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.185355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.139075 restraints weight = 17692.754| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.57 r_work: 0.2898 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 17211 Z= 0.148 Angle : 0.568 10.872 23497 Z= 0.263 Chirality : 0.044 0.154 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.586 89.536 2933 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.97 % Allowed : 15.10 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1963 helix: 2.58 (0.17), residues: 906 sheet: 0.61 (0.32), residues: 249 loop : -0.97 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 126 TYR 0.010 0.001 TYR E 7 PHE 0.015 0.001 PHE D 116 TRP 0.010 0.001 TRP J 142 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00374 (17191) covalent geometry : angle 0.56014 (23487) SS BOND : bond 0.00197 ( 2) SS BOND : angle 1.21683 ( 4) hydrogen bonds : bond 0.06499 ( 773) hydrogen bonds : angle 3.67861 ( 2259) metal coordination : bond 0.00935 ( 8) metal coordination : angle 5.78117 ( 6) Misc. bond : bond 0.05935 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8681 (mm) cc_final: 0.8413 (mt) REVERT: B 5 LYS cc_start: 0.7892 (tttt) cc_final: 0.7664 (tttm) REVERT: B 145 ILE cc_start: 0.8358 (mm) cc_final: 0.8019 (mm) REVERT: D 134 ASN cc_start: 0.7797 (p0) cc_final: 0.7514 (t0) REVERT: I 167 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7707 (mm-30) REVERT: J 20 LYS cc_start: 0.7961 (mtpp) cc_final: 0.7733 (mtmt) REVERT: K 55 MET cc_start: 0.6862 (mmt) cc_final: 0.6592 (mmt) REVERT: K 109 LYS cc_start: 0.7517 (mttm) cc_final: 0.6921 (mmmt) REVERT: L 127 CYS cc_start: 0.7746 (m) cc_final: 0.7423 (m) REVERT: N 30 ILE cc_start: 0.7679 (mt) cc_final: 0.7341 (mt) outliers start: 33 outliers final: 30 residues processed: 282 average time/residue: 0.0881 time to fit residues: 41.8699 Evaluate side-chains 294 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 96 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 188 optimal weight: 1.9990 chunk 180 optimal weight: 0.0770 chunk 146 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.186707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.139363 restraints weight = 17676.201| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.52 r_work: 0.2926 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 17211 Z= 0.124 Angle : 0.549 10.106 23497 Z= 0.253 Chirality : 0.043 0.201 2588 Planarity : 0.005 0.067 2839 Dihedral : 11.419 88.743 2933 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.03 % Allowed : 15.34 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 1963 helix: 2.64 (0.17), residues: 908 sheet: 0.62 (0.32), residues: 249 loop : -0.91 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 77 TYR 0.010 0.001 TYR B 80 PHE 0.011 0.001 PHE K 128 TRP 0.010 0.001 TRP J 142 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00306 (17191) covalent geometry : angle 0.54182 (23487) SS BOND : bond 0.00171 ( 2) SS BOND : angle 1.03076 ( 4) hydrogen bonds : bond 0.05825 ( 773) hydrogen bonds : angle 3.59515 ( 2259) metal coordination : bond 0.00748 ( 8) metal coordination : angle 5.40410 ( 6) Misc. bond : bond 0.05148 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8644 (mm) cc_final: 0.8418 (mt) REVERT: A 207 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7948 (ttm-80) REVERT: B 145 ILE cc_start: 0.8341 (mm) cc_final: 0.7998 (mm) REVERT: C 283 MET cc_start: 0.7011 (tpp) cc_final: 0.6746 (tpt) REVERT: D 134 ASN cc_start: 0.7758 (p0) cc_final: 0.7518 (t0) REVERT: I 136 TYR cc_start: 0.8765 (t80) cc_final: 0.8528 (t80) REVERT: I 167 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7691 (mm-30) REVERT: J 20 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7728 (mtmt) REVERT: K 55 MET cc_start: 0.6836 (mmt) cc_final: 0.6577 (mmt) REVERT: K 109 LYS cc_start: 0.7540 (mttm) cc_final: 0.6944 (mmmt) REVERT: K 111 ASN cc_start: 0.8636 (p0) cc_final: 0.8423 (p0) REVERT: L 127 CYS cc_start: 0.7781 (m) cc_final: 0.7472 (m) REVERT: N 30 ILE cc_start: 0.7678 (mt) cc_final: 0.7333 (mt) outliers start: 34 outliers final: 29 residues processed: 286 average time/residue: 0.0870 time to fit residues: 41.7461 Evaluate side-chains 287 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 57 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 64 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.185480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.137903 restraints weight = 17652.440| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.49 r_work: 0.2906 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 17211 Z= 0.146 Angle : 0.568 11.162 23497 Z= 0.262 Chirality : 0.044 0.232 2588 Planarity : 0.005 0.067 2839 Dihedral : 11.483 88.200 2933 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.91 % Allowed : 15.46 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1963 helix: 2.59 (0.17), residues: 908 sheet: 0.65 (0.33), residues: 249 loop : -0.93 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 126 TYR 0.010 0.001 TYR B 80 PHE 0.015 0.001 PHE D 116 TRP 0.010 0.001 TRP J 142 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00369 (17191) covalent geometry : angle 0.56087 (23487) SS BOND : bond 0.00191 ( 2) SS BOND : angle 1.20365 ( 4) hydrogen bonds : bond 0.06401 ( 773) hydrogen bonds : angle 3.62591 ( 2259) metal coordination : bond 0.00921 ( 8) metal coordination : angle 5.64968 ( 6) Misc. bond : bond 0.05855 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3926 Ramachandran restraints generated. 1963 Oldfield, 0 Emsley, 1963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8672 (mm) cc_final: 0.8410 (mt) REVERT: A 207 ARG cc_start: 0.8260 (ttt90) cc_final: 0.7998 (ttm-80) REVERT: B 101 MET cc_start: 0.6840 (ttm) cc_final: 0.6374 (mtp) REVERT: B 145 ILE cc_start: 0.8400 (mm) cc_final: 0.8060 (mm) REVERT: C 283 MET cc_start: 0.6972 (tpp) cc_final: 0.6718 (tpt) REVERT: D 134 ASN cc_start: 0.7759 (p0) cc_final: 0.7534 (t0) REVERT: I 167 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7715 (mm-30) REVERT: J 20 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7723 (mtmt) REVERT: K 55 MET cc_start: 0.6814 (mmt) cc_final: 0.6542 (mmt) REVERT: K 109 LYS cc_start: 0.7576 (mttm) cc_final: 0.6963 (mmmt) REVERT: K 111 ASN cc_start: 0.8649 (p0) cc_final: 0.8433 (p0) REVERT: L 127 CYS cc_start: 0.7760 (m) cc_final: 0.7456 (m) REVERT: N 30 ILE cc_start: 0.7703 (mt) cc_final: 0.7358 (mt) outliers start: 32 outliers final: 28 residues processed: 288 average time/residue: 0.0885 time to fit residues: 42.5633 Evaluate side-chains 298 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 96 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 15 optimal weight: 0.0040 chunk 166 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.187116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.139951 restraints weight = 17604.773| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.48 r_work: 0.2929 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 17211 Z= 0.118 Angle : 0.547 10.035 23497 Z= 0.251 Chirality : 0.043 0.252 2588 Planarity : 0.005 0.067 2839 Dihedral : 11.304 89.957 2933 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.79 % Allowed : 15.82 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 1963 helix: 2.67 (0.17), residues: 908 sheet: 0.68 (0.33), residues: 249 loop : -0.88 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 137 TYR 0.009 0.001 TYR B 80 PHE 0.010 0.001 PHE K 128 TRP 0.010 0.001 TRP J 142 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00287 (17191) covalent geometry : angle 0.53984 (23487) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.00726 ( 4) hydrogen bonds : bond 0.05674 ( 773) hydrogen bonds : angle 3.55983 ( 2259) metal coordination : bond 0.00733 ( 8) metal coordination : angle 5.40017 ( 6) Misc. bond : bond 0.04845 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.03 seconds wall clock time: 65 minutes 30.42 seconds (3930.42 seconds total)