Starting phenix.real_space_refine on Sat Jul 4 00:23:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tgg_55898/07_2026/9tgg_55898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tgg_55898/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9tgg_55898/07_2026/9tgg_55898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tgg_55898/07_2026/9tgg_55898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tgg_55898/07_2026/9tgg_55898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tgg_55898/07_2026/9tgg_55898.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 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: 4.46, per 1000 atoms: 0.27 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: 2.16 Conformation dependent library (CDL) restraints added in 803.5 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: 0.77 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: 3.42 Time building geometry restraints manager: 2.62 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 3.060 nonbonded pdb=" SG CYS Q 84 " pdb="CU CU Q 200 " model vdw 2.149 3.340 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: 6.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 21.130 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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/Z covalent geometry : bond 0.00477 / 0.22 (17191) covalent geometry : angle 0.70574 / 0.37 (23487) SS BOND : bond 0.00123 / 0.06 ( 2) SS BOND : angle 1.27652 / 0.66 ( 4) hydrogen bonds : bond 0.30082 / 19.82 ( 773) hydrogen bonds : angle 6.58525 / 4.80 ( 2259) metal coordination : bond 0.05176 / 2.66 ( 8) metal coordination : angle 11.57497 / 5.88 ( 6) Misc. bond : bond 0.07387 / 4.31 ( 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 : 0.480 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: 0.0996 time to fit residues: 57.4411 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 : 0.595 ------------------------------------------------------------------------------- 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... A 209 GLN ** C 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN I 177 GLN K 23 ASN K 153 ASN ** K 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3930 r_free = 0.3930 target = 0.183285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.133860 restraints weight = 17605.254| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.66 r_work: 0.2863 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 17211 Z= 0.189 Angle : 0.662 11.860 23497 Z= 0.316 Chirality : 0.047 0.162 2588 Planarity : 0.005 0.061 2839 Dihedral : 12.969 83.755 2941 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.91 % Allowed : 8.18 % 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: 0.94 (0.19), residues: 1963 helix: 2.23 (0.17), residues: 910 sheet: 0.07 (0.33), residues: 232 loop : -1.11 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 11 TYR 0.015 0.001 TYR B 80 PHE 0.017 0.002 PHE K 128 TRP 0.012 0.001 TRP D 164 HIS 0.008 0.002 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (17191) covalent geometry : angle 0.65234 / 0.32 (23487) SS BOND : bond 0.00227 / 0.11 ( 2) SS BOND : angle 1.55242 / 0.77 ( 4) hydrogen bonds : bond 0.08907 / 5.91 ( 773) hydrogen bonds : angle 4.47306 / 3.22 ( 2259) metal coordination : bond 0.01331 / 0.75 ( 8) metal coordination : angle 6.88701 / 3.34 ( 6) Misc. bond : bond 0.08154 / 4.90 ( 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 318 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8743 (mm) cc_final: 0.8490 (mt) REVERT: C 34 GLU cc_start: 0.7702 (tt0) cc_final: 0.7440 (tt0) REVERT: D 9 VAL cc_start: 0.8572 (m) cc_final: 0.8279 (p) REVERT: I 150 ILE cc_start: 0.8857 (mt) cc_final: 0.8517 (mp) REVERT: J 20 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7691 (mtmt) REVERT: K 109 LYS cc_start: 0.7603 (mttm) cc_final: 0.7174 (mmtt) REVERT: N 30 ILE cc_start: 0.8046 (mt) cc_final: 0.7725 (mt) REVERT: P 1 MET cc_start: 0.6640 (pmm) cc_final: 0.6249 (ptp) outliers start: 32 outliers final: 21 residues processed: 295 average time/residue: 0.1040 time to fit residues: 51.3865 Evaluate side-chains 290 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 L residue 69 LEU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 92 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 158 optimal weight: 0.0470 chunk 7 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 28 GLN K 232 ASN L 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.185270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.136628 restraints weight = 17920.057| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.77 r_work: 0.2895 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 17211 Z= 0.141 Angle : 0.576 10.423 23497 Z= 0.271 Chirality : 0.044 0.156 2588 Planarity : 0.005 0.063 2839 Dihedral : 12.416 85.644 2936 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.43 % Allowed : 11.70 % Favored : 86.87 % 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: 1.18 (0.19), residues: 1963 helix: 2.39 (0.17), residues: 910 sheet: 0.40 (0.34), residues: 218 loop : -0.99 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 11 TYR 0.010 0.001 TYR B 80 PHE 0.010 0.001 PHE A 131 TRP 0.010 0.001 TRP I 146 HIS 0.006 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (17191) covalent geometry : angle 0.56709 / 0.27 (23487) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 1.13768 / 0.56 ( 4) hydrogen bonds : bond 0.07127 / 4.75 ( 773) hydrogen bonds : angle 4.02736 / 2.88 ( 2259) metal coordination : bond 0.00857 / 0.50 ( 8) metal coordination : angle 6.39109 / 3.12 ( 6) Misc. bond : bond 0.06065 / 3.87 ( 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 311 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 287 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.9192 (mp) cc_final: 0.8949 (mm) REVERT: A 150 ILE cc_start: 0.8689 (mm) cc_final: 0.8466 (mt) REVERT: C 34 GLU cc_start: 0.7713 (tt0) cc_final: 0.7436 (tt0) REVERT: F 23 ILE cc_start: 0.8456 (mm) cc_final: 0.8219 (mm) REVERT: I 150 ILE cc_start: 0.8811 (mt) cc_final: 0.8474 (mp) REVERT: I 167 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7621 (mm-30) REVERT: I 201 MET cc_start: 0.8964 (mtp) cc_final: 0.8758 (mtm) REVERT: J 20 LYS cc_start: 0.7943 (mtpp) cc_final: 0.7721 (mtmt) REVERT: K 109 LYS cc_start: 0.7575 (mttm) cc_final: 0.7135 (mmtt) REVERT: K 111 ASN cc_start: 0.8630 (p0) cc_final: 0.8408 (p0) REVERT: L 97 THR cc_start: 0.8029 (m) cc_final: 0.7613 (t) REVERT: N 30 ILE cc_start: 0.7897 (mt) cc_final: 0.7624 (mt) REVERT: P 1 MET cc_start: 0.6369 (pmm) cc_final: 0.5928 (ptp) outliers start: 24 outliers final: 16 residues processed: 295 average time/residue: 0.1028 time to fit residues: 51.1275 Evaluate side-chains 287 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 63 THR 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 H residue 16 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 155 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain Q residue 92 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 53 optimal weight: 0.1980 chunk 135 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 28 GLN L 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.185436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.138113 restraints weight = 17755.466| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.75 r_work: 0.2887 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2288 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= 0.152 Angle : 0.577 10.552 23497 Z= 0.269 Chirality : 0.044 0.155 2588 Planarity : 0.005 0.065 2839 Dihedral : 12.223 88.348 2936 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.85 % Allowed : 12.72 % Favored : 85.43 % 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: 1.24 (0.19), residues: 1963 helix: 2.43 (0.17), residues: 912 sheet: 0.53 (0.34), residues: 218 loop : -0.99 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.015 0.001 TYR G 29 PHE 0.013 0.001 PHE K 128 TRP 0.010 0.001 TRP J 142 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (17191) covalent geometry : angle 0.56865 / 0.27 (23487) SS BOND : bond 0.00217 / 0.11 ( 2) SS BOND : angle 1.29968 / 0.64 ( 4) hydrogen bonds : bond 0.06991 / 4.63 ( 773) hydrogen bonds : angle 3.90438 / 2.79 ( 2259) metal coordination : bond 0.00948 / 0.53 ( 8) metal coordination : angle 6.18755 / 2.99 ( 6) Misc. bond : bond 0.06634 / 4.26 ( 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 312 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8687 (mm) cc_final: 0.8484 (mt) REVERT: C 34 GLU cc_start: 0.7719 (tt0) cc_final: 0.7468 (tt0) REVERT: I 167 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7657 (mm-30) REVERT: J 20 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7759 (mtmt) REVERT: K 109 LYS cc_start: 0.7605 (mttm) cc_final: 0.7138 (mmtt) REVERT: K 111 ASN cc_start: 0.8665 (p0) cc_final: 0.8425 (p0) REVERT: L 97 THR cc_start: 0.8015 (m) cc_final: 0.7598 (t) REVERT: N 30 ILE cc_start: 0.7841 (mt) cc_final: 0.7476 (mt) REVERT: P 1 MET cc_start: 0.6080 (pmm) cc_final: 0.5650 (ptp) outliers start: 31 outliers final: 24 residues processed: 292 average time/residue: 0.1032 time to fit residues: 50.5194 Evaluate side-chains 298 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 40 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 98 LEU 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 H residue 16 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 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 K residue 280 LEU Chi-restraints excluded: chain L residue 27 SER 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: 10.0000 chunk 28 optimal weight: 0.0070 chunk 85 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 0.0770 chunk 99 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 32 optimal weight: 0.0870 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 GLN G 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.187664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.143635 restraints weight = 17752.921| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.69 r_work: 0.2928 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 17211 Z= 0.110 Angle : 0.535 9.366 23497 Z= 0.250 Chirality : 0.042 0.150 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.804 89.837 2933 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 13.97 % Favored : 84.54 % 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: 1.41 (0.19), residues: 1963 helix: 2.59 (0.17), residues: 912 sheet: 0.64 (0.35), residues: 214 loop : -0.93 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.012 0.001 TYR G 29 PHE 0.010 0.001 PHE I 52 TRP 0.009 0.001 TRP J 142 HIS 0.003 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (17191) covalent geometry : angle 0.52729 / 0.25 (23487) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 0.88917 / 0.44 ( 4) hydrogen bonds : bond 0.05597 / 3.74 ( 773) hydrogen bonds : angle 3.72223 / 2.66 ( 2259) metal coordination : bond 0.00625 / 0.39 ( 8) metal coordination : angle 5.56241 / 2.69 ( 6) Misc. bond : bond 0.04845 / 3.10 ( 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 308 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 283 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ILE cc_start: 0.8631 (mm) cc_final: 0.8397 (mt) REVERT: A 207 ARG cc_start: 0.8149 (ttt90) cc_final: 0.7915 (ttm-80) REVERT: C 34 GLU cc_start: 0.7668 (tt0) cc_final: 0.7448 (tt0) REVERT: F 23 ILE cc_start: 0.8367 (mm) cc_final: 0.8152 (mm) REVERT: I 167 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7676 (mm-30) REVERT: J 20 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7738 (mtmt) REVERT: K 109 LYS cc_start: 0.7485 (mttm) cc_final: 0.6976 (mmtt) REVERT: K 111 ASN cc_start: 0.8590 (p0) cc_final: 0.8382 (p0) REVERT: L 97 THR cc_start: 0.7892 (m) cc_final: 0.7497 (t) REVERT: L 127 CYS cc_start: 0.7889 (m) cc_final: 0.7550 (m) REVERT: N 30 ILE cc_start: 0.7671 (mt) cc_final: 0.7353 (mt) outliers start: 25 outliers final: 15 residues processed: 295 average time/residue: 0.1061 time to fit residues: 52.5897 Evaluate side-chains 295 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 154 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain I residue 131 PHE 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 27 SER Chi-restraints excluded: chain L residue 63 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: 0.5980 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 133 optimal weight: 7.9990 chunk 22 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 123 optimal weight: 0.0040 chunk 153 optimal weight: 0.8980 chunk 146 optimal weight: 7.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 274 GLN L 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.187364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.140113 restraints weight = 17711.285| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.62 r_work: 0.2939 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 17211 Z= 0.115 Angle : 0.538 9.769 23497 Z= 0.249 Chirality : 0.043 0.153 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.526 88.538 2933 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.61 % Allowed : 14.93 % Favored : 83.46 % 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: 1.53 (0.19), residues: 1963 helix: 2.63 (0.17), residues: 920 sheet: 0.72 (0.34), residues: 225 loop : -0.83 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 137 TYR 0.011 0.001 TYR C 190 PHE 0.013 0.001 PHE D 116 TRP 0.010 0.001 TRP J 142 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (17191) covalent geometry : angle 0.53121 / 0.25 (23487) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 0.98548 / 0.48 ( 4) hydrogen bonds : bond 0.05592 / 3.70 ( 773) hydrogen bonds : angle 3.60543 / 2.57 ( 2259) metal coordination : bond 0.00698 / 0.41 ( 8) metal coordination : angle 5.19990 / 2.47 ( 6) Misc. bond : bond 0.05003 / 3.16 ( 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 298 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 271 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8983 (tpt) cc_final: 0.8704 (tpt) REVERT: A 150 ILE cc_start: 0.8638 (mm) cc_final: 0.8418 (mt) REVERT: A 207 ARG cc_start: 0.8171 (ttt90) cc_final: 0.7900 (ttm-80) REVERT: D 134 ASN cc_start: 0.7848 (p0) cc_final: 0.7466 (t0) REVERT: F 23 ILE cc_start: 0.8357 (mm) cc_final: 0.8144 (mm) REVERT: I 167 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7695 (mm-30) REVERT: J 20 LYS cc_start: 0.7977 (mtpp) cc_final: 0.7759 (mtmt) REVERT: K 109 LYS cc_start: 0.7512 (mttm) cc_final: 0.6918 (mmmt) REVERT: K 111 ASN cc_start: 0.8604 (p0) cc_final: 0.8369 (p0) REVERT: L 97 THR cc_start: 0.7867 (m) cc_final: 0.7474 (t) REVERT: L 127 CYS cc_start: 0.7813 (m) cc_final: 0.7499 (m) REVERT: N 30 ILE cc_start: 0.7653 (mt) cc_final: 0.7330 (mt) outliers start: 27 outliers final: 21 residues processed: 286 average time/residue: 0.1045 time to fit residues: 50.4051 Evaluate side-chains 288 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 179 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 131 PHE 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 L residue 12 MET Chi-restraints excluded: chain L residue 23 LEU 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 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: 0.0030 chunk 126 optimal weight: 2.9990 chunk 112 optimal weight: 0.0030 chunk 172 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.187384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.140073 restraints weight = 17664.234| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.50 r_work: 0.2949 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 17211 Z= 0.117 Angle : 0.540 9.968 23497 Z= 0.248 Chirality : 0.042 0.150 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.381 89.022 2933 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.73 % Allowed : 14.99 % Favored : 83.28 % 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: 1.55 (0.19), residues: 1963 helix: 2.63 (0.17), residues: 922 sheet: 0.54 (0.33), residues: 251 loop : -0.81 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 126 TYR 0.010 0.001 TYR B 80 PHE 0.011 0.001 PHE I 52 TRP 0.010 0.001 TRP J 142 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (17191) covalent geometry : angle 0.53317 / 0.25 (23487) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 0.97949 / 0.47 ( 4) hydrogen bonds : bond 0.05541 / 3.67 ( 773) hydrogen bonds : angle 3.56893 / 2.55 ( 2259) metal coordination : bond 0.00715 / 0.42 ( 8) metal coordination : angle 5.22004 / 2.47 ( 6) Misc. bond : bond 0.04497 / 2.88 ( 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 299 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 270 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8962 (tpt) cc_final: 0.8668 (tpt) REVERT: A 150 ILE cc_start: 0.8624 (mm) cc_final: 0.8415 (mt) REVERT: B 5 LYS cc_start: 0.7973 (tttt) cc_final: 0.7741 (tttm) REVERT: D 134 ASN cc_start: 0.7810 (p0) cc_final: 0.7481 (t0) REVERT: F 23 ILE cc_start: 0.8374 (mm) cc_final: 0.8158 (mm) REVERT: I 167 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7660 (mm-30) REVERT: J 20 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7741 (mtmt) REVERT: K 109 LYS cc_start: 0.7524 (mttm) cc_final: 0.6968 (mmtt) REVERT: K 111 ASN cc_start: 0.8613 (p0) cc_final: 0.8375 (p0) REVERT: L 97 THR cc_start: 0.7902 (m) cc_final: 0.7517 (t) REVERT: L 127 CYS cc_start: 0.7786 (m) cc_final: 0.7481 (m) REVERT: N 30 ILE cc_start: 0.7679 (mt) cc_final: 0.7354 (mt) outliers start: 29 outliers final: 24 residues processed: 285 average time/residue: 0.1056 time to fit residues: 50.6150 Evaluate side-chains 290 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 40 LEU Chi-restraints excluded: chain C residue 179 VAL 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 178 SER 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 23 LEU 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 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: 0.6980 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 80 optimal weight: 0.0270 chunk 127 optimal weight: 8.9990 chunk 69 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 189 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.187238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139676 restraints weight = 17710.819| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.44 r_work: 0.2947 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 17211 Z= 0.120 Angle : 0.545 10.311 23497 Z= 0.250 Chirality : 0.043 0.153 2588 Planarity : 0.005 0.066 2839 Dihedral : 11.306 89.729 2933 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 15.40 % 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: 1.57 (0.19), residues: 1963 helix: 2.71 (0.17), residues: 910 sheet: 0.66 (0.33), residues: 249 loop : -0.87 (0.21), residues: 804 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 0.016 0.001 PHE D 116 TRP 0.010 0.001 TRP J 142 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (17191) covalent geometry : angle 0.53866 / 0.25 (23487) SS BOND : bond 0.00152 / 0.08 ( 2) SS BOND : angle 1.01570 / 0.49 ( 4) hydrogen bonds : bond 0.05641 / 3.72 ( 773) hydrogen bonds : angle 3.55111 / 2.54 ( 2259) metal coordination : bond 0.00744 / 0.43 ( 8) metal coordination : angle 5.10790 / 2.41 ( 6) Misc. bond : bond 0.04689 / 3.03 ( 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 309 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8966 (tpt) cc_final: 0.8716 (tpt) REVERT: A 150 ILE cc_start: 0.8613 (mm) cc_final: 0.8406 (mt) REVERT: B 5 LYS cc_start: 0.7977 (tttt) cc_final: 0.7740 (tttm) REVERT: B 101 MET cc_start: 0.6755 (ttm) cc_final: 0.6266 (mtp) REVERT: D 134 ASN cc_start: 0.7765 (p0) cc_final: 0.7494 (t0) REVERT: F 23 ILE cc_start: 0.8387 (mm) cc_final: 0.8184 (mm) REVERT: I 167 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7668 (mm-30) REVERT: J 20 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7725 (mtmt) REVERT: K 109 LYS cc_start: 0.7498 (mttm) cc_final: 0.6877 (mmmm) REVERT: L 127 CYS cc_start: 0.7753 (m) cc_final: 0.7450 (m) REVERT: N 30 ILE cc_start: 0.7638 (mt) cc_final: 0.7309 (mt) outliers start: 33 outliers final: 28 residues processed: 293 average time/residue: 0.1015 time to fit residues: 49.7971 Evaluate side-chains 293 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 C residue 183 VAL 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 56 PHE Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 178 SER 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 K residue 97 MET Chi-restraints excluded: chain L residue 12 MET Chi-restraints excluded: chain L residue 23 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 188 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.186050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.138452 restraints weight = 17640.469| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.46 r_work: 0.2921 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 17211 Z= 0.141 Angle : 0.572 13.860 23497 Z= 0.262 Chirality : 0.044 0.263 2588 Planarity : 0.005 0.067 2839 Dihedral : 11.364 89.151 2933 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 15.52 % Favored : 82.75 % 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: 2.65 (0.17), residues: 908 sheet: 0.67 (0.33), residues: 249 loop : -0.85 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 126 TYR 0.013 0.001 TYR E 7 PHE 0.014 0.001 PHE I 52 TRP 0.010 0.001 TRP J 142 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.14 (17191) covalent geometry : angle 0.56583 / 0.26 (23487) SS BOND : bond 0.00189 / 0.09 ( 2) SS BOND : angle 1.16683 / 0.56 ( 4) hydrogen bonds : bond 0.06190 / 4.08 ( 773) hydrogen bonds : angle 3.58410 / 2.57 ( 2259) metal coordination : bond 0.00878 / 0.50 ( 8) metal coordination : angle 5.40438 / 2.52 ( 6) Misc. bond : bond 0.05064 / 3.34 ( 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 303 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8993 (tpt) cc_final: 0.8666 (tpt) REVERT: A 150 ILE cc_start: 0.8643 (mm) cc_final: 0.8408 (mt) REVERT: A 207 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7967 (ttm-80) REVERT: B 5 LYS cc_start: 0.7978 (tttt) cc_final: 0.7757 (tttm) REVERT: B 145 ILE cc_start: 0.8321 (mm) cc_final: 0.7984 (mm) REVERT: D 134 ASN cc_start: 0.7735 (p0) cc_final: 0.7514 (t0) REVERT: I 167 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7667 (mm-30) REVERT: J 20 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7714 (mtmt) REVERT: K 109 LYS cc_start: 0.7521 (mttm) cc_final: 0.6960 (mmmt) REVERT: L 127 CYS cc_start: 0.7741 (m) cc_final: 0.7427 (m) REVERT: N 30 ILE cc_start: 0.7667 (mt) cc_final: 0.7333 (mt) outliers start: 29 outliers final: 24 residues processed: 288 average time/residue: 0.1046 time to fit residues: 50.4470 Evaluate side-chains 296 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 84 VAL 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 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 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 57 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 126 optimal weight: 0.0010 chunk 52 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 158 GLN L 72 HIS L 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.185598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138695 restraints weight = 17649.020| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.50 r_work: 0.2914 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 17211 Z= 0.143 Angle : 0.576 12.418 23497 Z= 0.264 Chirality : 0.044 0.239 2588 Planarity : 0.005 0.067 2839 Dihedral : 11.389 88.906 2933 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.61 % Allowed : 15.82 % Favored : 82.57 % 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: 1.49 (0.19), residues: 1963 helix: 2.61 (0.17), residues: 906 sheet: 0.71 (0.33), residues: 249 loop : -0.87 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 126 TYR 0.012 0.001 TYR E 7 PHE 0.013 0.001 PHE D 116 TRP 0.010 0.001 TRP J 142 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.14 (17191) covalent geometry : angle 0.56904 / 0.26 (23487) SS BOND : bond 0.00180 / 0.09 ( 2) SS BOND : angle 1.16595 / 0.56 ( 4) hydrogen bonds : bond 0.06299 / 4.15 ( 773) hydrogen bonds : angle 3.61389 / 2.59 ( 2259) metal coordination : bond 0.00881 / 0.50 ( 8) metal coordination : angle 5.45003 / 2.54 ( 6) Misc. bond : bond 0.05009 / 3.32 ( 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 300 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 273 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.8959 (tpt) cc_final: 0.8702 (tpt) REVERT: A 150 ILE cc_start: 0.8619 (mm) cc_final: 0.8389 (mt) REVERT: B 101 MET cc_start: 0.6865 (ttm) cc_final: 0.6171 (mtp) REVERT: B 145 ILE cc_start: 0.8354 (mm) cc_final: 0.8019 (mm) REVERT: F 30 ILE cc_start: 0.7439 (mt) cc_final: 0.7190 (mt) REVERT: I 167 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7667 (mm-30) REVERT: J 20 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7727 (mtmt) REVERT: J 134 LEU cc_start: 0.8606 (mm) cc_final: 0.8354 (mt) REVERT: K 109 LYS cc_start: 0.7513 (mttm) cc_final: 0.6934 (mmmt) REVERT: L 127 CYS cc_start: 0.7724 (m) cc_final: 0.7408 (m) REVERT: N 30 ILE cc_start: 0.7660 (mt) cc_final: 0.7320 (mt) outliers start: 27 outliers final: 23 residues processed: 288 average time/residue: 0.1063 time to fit residues: 50.8982 Evaluate side-chains 294 residues out of total 1675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 40 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 98 LEU 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 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 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: 0.0470 chunk 166 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 146 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 180 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 159 optimal weight: 0.0060 chunk 68 optimal weight: 10.0000 overall best weight: 0.4294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.187071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.140014 restraints weight = 17571.916| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.48 r_work: 0.2939 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 17211 Z= 0.118 Angle : 0.555 10.188 23497 Z= 0.256 Chirality : 0.043 0.247 2588 Planarity : 0.005 0.067 2839 Dihedral : 11.287 89.113 2933 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.49 % Allowed : 15.82 % Favored : 82.69 % 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: 1.57 (0.19), residues: 1963 helix: 2.67 (0.17), residues: 908 sheet: 0.72 (0.33), residues: 249 loop : -0.82 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 26 TYR 0.009 0.001 TYR B 80 PHE 0.011 0.001 PHE I 52 TRP 0.010 0.001 TRP J 142 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (17191) covalent geometry : angle 0.54897 / 0.26 (23487) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 0.97244 / 0.47 ( 4) hydrogen bonds : bond 0.05658 / 3.74 ( 773) hydrogen bonds : angle 3.55874 / 2.55 ( 2259) metal coordination : bond 0.00720 / 0.42 ( 8) metal coordination : angle 5.17917 / 2.44 ( 6) Misc. bond : bond 0.04345 / 2.84 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4422.18 seconds wall clock time: 76 minutes 40.54 seconds (4600.54 seconds total)