Starting phenix.real_space_refine on Thu Sep 18 11:13:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9es9_19940/09_2025/9es9_19940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9es9_19940/09_2025/9es9_19940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9es9_19940/09_2025/9es9_19940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9es9_19940/09_2025/9es9_19940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9es9_19940/09_2025/9es9_19940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9es9_19940/09_2025/9es9_19940.map" } resolution = 2.33 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= 0.001 sd= 0.034 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 Br 4 7.06 5 Mg 2 5.21 5 S 72 5.16 5 C 10774 2.51 5 N 2530 2.21 5 O 3056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16450 Number of models: 1 Model: "" Number of chains: 26 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: 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: "C" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2168 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1334 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 164} 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: 280 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Conformer: "B" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} bond proxies already assigned to first conformer: 257 Chain: "G" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'BNT': 1, 'HEC': 1, 'HEM': 2, 'LMG': 1, 'UMQ': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 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: "H" 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: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5869 SG CYS D 107 105.888 53.723 42.098 1.00 88.59 S ATOM 6005 SG CYS D 125 105.767 57.619 42.247 1.00 68.61 S Restraints were copied for chains: I, J, K, L, M, N, O, P, R Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE F 7 " occ=0.60 ... (20 atoms not shown) pdb=" CZ BPHE F 7 " occ=0.40 residue: pdb=" N APHE N 7 " occ=0.60 ... (20 atoms not shown) pdb=" CZ BPHE N 7 " occ=0.40 Time building chain proxies: 4.02, per 1000 atoms: 0.24 Number of scatterers: 16450 At special positions: 0 Unit cell: (148.78, 116.1, 117.82, 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) Br 4 34.99 Fe 12 26.01 S 72 16.00 Mg 2 11.99 O 3056 8.00 N 2530 7.00 C 10774 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 699.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 125 " pdb=" FES L 202 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 109 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 107 " Number of angles added : 6 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 14 sheets defined 51.2% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.084A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.547A 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: 3.588A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 137 removed outlier: 3.537A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.508A pdb=" N LYS A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.524A pdb=" N LEU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 189 through 210 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.680A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 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 91 removed outlier: 3.500A pdb=" N ARG B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.824A 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 147 Processing helix chain 'B' and resid 148 through 149 No H-bonds generated for 'chain 'B' and resid 148 through 149' Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.667A pdb=" N ILE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.542A pdb=" N GLU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.520A pdb=" N ILE C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 removed outlier: 3.973A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.588A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.500A pdb=" N ILE E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 37 removed outlier: 3.579A pdb=" N ASN F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.626A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.772A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.084A 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: 3.547A 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: 3.588A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.537A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.508A pdb=" N LYS I 149 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 158 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.524A pdb=" N LEU I 168 " --> pdb=" O PRO I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.680A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 58 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 91 removed outlier: 3.500A pdb=" N ARG J 89 " --> pdb=" O PHE J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 109 removed outlier: 3.824A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.668A pdb=" N ILE K 89 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.542A pdb=" N GLU K 95 " --> pdb=" O PRO K 91 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.520A pdb=" N ILE K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE K 256 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL K 269 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 removed outlier: 3.973A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix Proline residue: L 36 - end of helix Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.588A pdb=" N LYS L 70 " --> pdb=" O ALA L 66 " (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 removed outlier: 3.511A pdb=" N ILE M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 37 removed outlier: 3.579A pdb=" N ASN N 14 " --> pdb=" O ALA N 10 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU N 36 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 37 " --> pdb=" O THR N 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 32 removed outlier: 3.626A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 26 removed outlier: 3.772A pdb=" N LEU P 19 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 removed outlier: 3.513A pdb=" N LYS Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 43 removed outlier: 3.513A pdb=" N LYS R 41 " --> pdb=" O TRP R 37 " (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: 3.727A 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: 6.191A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 106 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASN C 111 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N SER C 104 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'C' and resid 203 through 207 removed outlier: 3.505A pdb=" N GLU C 191 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS C 181 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 219 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.683A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.628A pdb=" N ARG D 140 " --> pdb=" O GLN D 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.728A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.191A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG K 106 " --> pdb=" O LYS K 109 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASN K 111 " --> pdb=" O SER K 104 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N SER K 104 " --> pdb=" O ASN K 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'K' and resid 203 through 207 removed outlier: 3.505A pdb=" N GLU K 191 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS K 181 " --> pdb=" O ASN K 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU K 219 " --> pdb=" O VAL K 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.683A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117 removed outlier: 3.627A pdb=" N ARG L 140 " --> pdb=" O GLN L 131 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.91 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: 6358 1.39 - 1.59: 10180 1.59 - 1.79: 46 1.79 - 2.00: 72 2.00 - 2.20: 48 Bond restraints: 16704 Sorted by residual: 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 6.25e+00 bond pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N LYS Q 32 " pdb=" CA LYS Q 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N LYS R 32 " pdb=" CA LYS R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 16699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 22683 2.76 - 5.51: 167 5.51 - 8.27: 2 8.27 - 11.02: 0 11.02 - 13.78: 2 Bond angle restraints: 22854 Sorted by residual: angle pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sigma weight residual 109.00 122.78 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sigma weight residual 109.00 122.78 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C GLN C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.83 125.21 -3.38 1.56e+00 4.11e-01 4.69e+00 angle pdb=" C GLN K 246 " pdb=" N ASP K 247 " pdb=" CA ASP K 247 " ideal model delta sigma weight residual 121.83 125.14 -3.31 1.56e+00 4.11e-01 4.51e+00 angle pdb=" CA GLY L 102 " pdb=" C GLY L 102 " pdb=" N ILE L 103 " ideal model delta sigma weight residual 114.75 117.71 -2.96 1.40e+00 5.10e-01 4.47e+00 ... (remaining 22849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 9393 21.46 - 42.92: 323 42.92 - 64.38: 68 64.38 - 85.85: 24 85.85 - 107.31: 6 Dihedral angle restraints: 9814 sinusoidal: 4188 harmonic: 5626 Sorted by residual: dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 8.21 51.79 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2C HEC I 303 " pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sinusoidal sigma weight residual 60.00 8.21 51.79 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2B HEC I 303 " pdb=" C3B HEC I 303 " pdb=" CAB HEC I 303 " pdb=" CBB HEC I 303 " ideal model delta sinusoidal sigma weight residual -120.00 -74.11 -45.89 2 1.00e+01 1.00e-02 2.47e+01 ... (remaining 9811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1441 0.027 - 0.053: 677 0.053 - 0.080: 238 0.080 - 0.107: 116 0.107 - 0.133: 80 Chirality restraints: 2552 Sorted by residual: chirality pdb=" CA ILE G 2 " pdb=" N ILE G 2 " pdb=" C ILE G 2 " pdb=" CB ILE G 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE O 2 " pdb=" N ILE O 2 " pdb=" C ILE O 2 " pdb=" CB ILE O 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE K 51 " pdb=" N ILE K 51 " pdb=" C ILE K 51 " pdb=" CB ILE K 51 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2549 not shown) Planarity restraints: 2806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 162 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO L 163 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 163 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 163 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 162 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO D 163 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 146 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO K 147 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO K 147 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 147 " 0.020 5.00e-02 4.00e+02 ... (remaining 2803 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 127 2.58 - 3.16: 13129 3.16 - 3.74: 22884 3.74 - 4.32: 34341 4.32 - 4.90: 57244 Nonbonded interactions: 127725 Sorted by model distance: nonbonded pdb=" OD2 ASP B 35 " pdb=" O HOH B 301 " model vdw 1.994 3.040 nonbonded pdb=" OD2 ASP J 35 " pdb=" O HOH J 301 " model vdw 1.996 3.040 nonbonded pdb=" OD1 ASP J 35 " pdb=" O HOH J 302 " model vdw 2.022 3.040 nonbonded pdb=" OD1 ASP B 35 " pdb=" O HOH B 302 " model vdw 2.023 3.040 nonbonded pdb=" O HOH K 413 " pdb=" O HOH K 422 " model vdw 2.067 3.040 ... (remaining 127720 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' 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' } ncs_group { reference = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.011 0.737 16728 Z= 0.273 Angle : 0.543 13.775 22864 Z= 0.243 Chirality : 0.042 0.133 2552 Planarity : 0.004 0.061 2806 Dihedral : 12.293 107.306 6204 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.61 % Allowed : 2.66 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.37 (0.19), residues: 1940 helix: 1.22 (0.16), residues: 924 sheet: -0.51 (0.32), residues: 258 loop : -0.62 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 18 TYR 0.010 0.001 TYR I 136 PHE 0.011 0.001 PHE C 128 TRP 0.008 0.001 TRP L 164 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00349 (16704) covalent geometry : angle 0.53369 (22854) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.16426 ( 4) hydrogen bonds : bond 0.31861 ( 805) hydrogen bonds : angle 6.36779 ( 2285) metal coordination : bond 0.02083 ( 8) metal coordination : angle 6.29373 ( 6) Misc. bond : bond 0.35219 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.666 Fit side-chains REVERT: A 75 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 156 ASP cc_start: 0.8624 (t0) cc_final: 0.8270 (t0) REVERT: C 181 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8897 (ttpp) REVERT: D 8 ASN cc_start: 0.8745 (t0) cc_final: 0.8243 (t0) REVERT: I 75 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: I 156 ASP cc_start: 0.8624 (t0) cc_final: 0.8269 (t0) REVERT: K 56 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7722 (mm110) REVERT: L 8 ASN cc_start: 0.8746 (t0) cc_final: 0.8241 (t0) outliers start: 10 outliers final: 7 residues processed: 210 average time/residue: 0.8120 time to fit residues: 184.3065 Evaluate side-chains 177 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 99 ASN D 121 ASN J 118 ASN K 99 ASN L 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.068799 restraints weight = 46486.639| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.81 r_work: 0.2817 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 16728 Z= 0.171 Angle : 0.682 9.602 22864 Z= 0.325 Chirality : 0.046 0.168 2552 Planarity : 0.005 0.067 2806 Dihedral : 12.106 93.169 2700 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.97 % Allowed : 7.08 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.36 (0.20), residues: 1940 helix: 2.26 (0.17), residues: 968 sheet: -0.00 (0.33), residues: 238 loop : -0.65 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 137 TYR 0.012 0.001 TYR A 136 PHE 0.014 0.002 PHE M 2 TRP 0.009 0.001 TRP A 146 HIS 0.006 0.001 HIS L 151 Details of bonding type rmsd covalent geometry : bond 0.00362 (16704) covalent geometry : angle 0.67442 (22854) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.94703 ( 4) hydrogen bonds : bond 0.10000 ( 805) hydrogen bonds : angle 4.31238 ( 2285) metal coordination : bond 0.00441 ( 8) metal coordination : angle 6.09524 ( 6) Misc. bond : bond 0.10639 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.719 Fit side-chains REVERT: A 156 ASP cc_start: 0.8972 (t0) cc_final: 0.8586 (t0) REVERT: C 181 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8733 (ttpp) REVERT: D 8 ASN cc_start: 0.8679 (t0) cc_final: 0.8136 (t0) REVERT: I 156 ASP cc_start: 0.8981 (t0) cc_final: 0.8596 (t0) REVERT: L 8 ASN cc_start: 0.8681 (t0) cc_final: 0.8132 (t0) REVERT: Q 50 GLU cc_start: 0.7944 (tt0) cc_final: 0.7712 (tt0) outliers start: 16 outliers final: 6 residues processed: 177 average time/residue: 0.8228 time to fit residues: 157.0322 Evaluate side-chains 158 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN D 121 ASN J 118 ASN L 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.070798 restraints weight = 47880.952| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.84 r_work: 0.2857 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 16728 Z= 0.142 Angle : 0.612 9.406 22864 Z= 0.285 Chirality : 0.044 0.166 2552 Planarity : 0.005 0.068 2806 Dihedral : 10.947 84.066 2692 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.88 % Allowed : 7.75 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.51 (0.20), residues: 1940 helix: 2.53 (0.17), residues: 968 sheet: 0.09 (0.32), residues: 238 loop : -0.83 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 50 TYR 0.008 0.001 TYR I 105 PHE 0.011 0.001 PHE I 131 TRP 0.009 0.001 TRP I 118 HIS 0.005 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00309 (16704) covalent geometry : angle 0.60431 (22854) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.87086 ( 4) hydrogen bonds : bond 0.08238 ( 805) hydrogen bonds : angle 3.94938 ( 2285) metal coordination : bond 0.00309 ( 8) metal coordination : angle 5.85675 ( 6) Misc. bond : bond 0.08600 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.635 Fit side-chains REVERT: A 75 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8121 (mp0) REVERT: A 131 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7082 (t80) REVERT: A 156 ASP cc_start: 0.8975 (t0) cc_final: 0.8560 (t0) REVERT: C 181 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8767 (ttpp) REVERT: D 8 ASN cc_start: 0.8731 (t0) cc_final: 0.8174 (t0) REVERT: E 27 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7997 (tptm) REVERT: I 75 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: I 131 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.7082 (t80) REVERT: I 156 ASP cc_start: 0.8976 (t0) cc_final: 0.8559 (t0) REVERT: L 8 ASN cc_start: 0.8729 (t0) cc_final: 0.8164 (t0) REVERT: M 27 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.8002 (tptm) REVERT: Q 50 GLU cc_start: 0.7791 (tt0) cc_final: 0.7495 (tt0) outliers start: 31 outliers final: 10 residues processed: 182 average time/residue: 0.8132 time to fit residues: 159.5979 Evaluate side-chains 168 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.069105 restraints weight = 40982.114| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.67 r_work: 0.2824 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 16728 Z= 0.162 Angle : 0.635 9.701 22864 Z= 0.297 Chirality : 0.045 0.156 2552 Planarity : 0.005 0.069 2806 Dihedral : 11.026 84.234 2692 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.51 % Allowed : 9.02 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.47 (0.19), residues: 1940 helix: 2.52 (0.17), residues: 968 sheet: 0.04 (0.32), residues: 238 loop : -0.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 50 TYR 0.009 0.001 TYR A 105 PHE 0.014 0.002 PHE K 128 TRP 0.009 0.001 TRP L 164 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00378 (16704) covalent geometry : angle 0.62838 (22854) SS BOND : bond 0.00195 ( 2) SS BOND : angle 1.12238 ( 4) hydrogen bonds : bond 0.08866 ( 805) hydrogen bonds : angle 3.92806 ( 2285) metal coordination : bond 0.00413 ( 8) metal coordination : angle 5.66780 ( 6) Misc. bond : bond 0.10082 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.564 Fit side-chains REVERT: A 75 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: A 156 ASP cc_start: 0.8973 (t0) cc_final: 0.8521 (t0) REVERT: C 181 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8748 (ttpp) REVERT: D 8 ASN cc_start: 0.8738 (t0) cc_final: 0.8182 (t0) REVERT: E 27 LYS cc_start: 0.8188 (tptt) cc_final: 0.7969 (tptm) REVERT: I 75 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: I 156 ASP cc_start: 0.8977 (t0) cc_final: 0.8523 (t0) REVERT: L 8 ASN cc_start: 0.8733 (t0) cc_final: 0.8174 (t0) REVERT: M 27 LYS cc_start: 0.8190 (tptt) cc_final: 0.7969 (tptm) outliers start: 25 outliers final: 15 residues processed: 175 average time/residue: 0.8823 time to fit residues: 166.4538 Evaluate side-chains 165 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 56 GLN D 121 ASN J 118 ASN L 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067175 restraints weight = 55507.992| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.04 r_work: 0.2780 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 16728 Z= 0.179 Angle : 0.660 9.694 22864 Z= 0.310 Chirality : 0.046 0.150 2552 Planarity : 0.005 0.070 2806 Dihedral : 11.060 84.385 2692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.00 % Allowed : 9.50 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.38 (0.19), residues: 1940 helix: 2.48 (0.17), residues: 968 sheet: -0.04 (0.33), residues: 230 loop : -0.94 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 184 TYR 0.010 0.001 TYR A 105 PHE 0.015 0.002 PHE K 128 TRP 0.011 0.001 TRP L 164 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00431 (16704) covalent geometry : angle 0.65342 (22854) SS BOND : bond 0.00205 ( 2) SS BOND : angle 1.28543 ( 4) hydrogen bonds : bond 0.09411 ( 805) hydrogen bonds : angle 3.95342 ( 2285) metal coordination : bond 0.00382 ( 8) metal coordination : angle 5.55022 ( 6) Misc. bond : bond 0.10699 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.595 Fit side-chains REVERT: A 75 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: A 156 ASP cc_start: 0.8999 (t0) cc_final: 0.8564 (t0) REVERT: C 181 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8725 (ttpp) REVERT: D 8 ASN cc_start: 0.8778 (t0) cc_final: 0.8208 (t0) REVERT: E 27 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7965 (tptm) REVERT: I 75 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: I 156 ASP cc_start: 0.9004 (t0) cc_final: 0.8568 (t0) REVERT: L 8 ASN cc_start: 0.8771 (t0) cc_final: 0.8197 (t0) REVERT: M 27 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7965 (tptm) outliers start: 33 outliers final: 16 residues processed: 181 average time/residue: 0.8418 time to fit residues: 164.4831 Evaluate side-chains 168 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 120 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 176 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 56 GLN K 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.106916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.068091 restraints weight = 47627.093| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.86 r_work: 0.2800 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 16728 Z= 0.166 Angle : 0.643 9.532 22864 Z= 0.303 Chirality : 0.045 0.148 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.970 84.180 2692 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.30 % Allowed : 9.62 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.42 (0.19), residues: 1940 helix: 2.51 (0.17), residues: 968 sheet: -0.03 (0.32), residues: 238 loop : -0.93 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 184 TYR 0.009 0.001 TYR A 105 PHE 0.013 0.002 PHE K 128 TRP 0.010 0.001 TRP L 164 HIS 0.007 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00394 (16704) covalent geometry : angle 0.63747 (22854) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.14319 ( 4) hydrogen bonds : bond 0.08993 ( 805) hydrogen bonds : angle 3.91912 ( 2285) metal coordination : bond 0.00386 ( 8) metal coordination : angle 5.39548 ( 6) Misc. bond : bond 0.10242 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.496 Fit side-chains REVERT: A 75 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: A 156 ASP cc_start: 0.8983 (t0) cc_final: 0.8567 (t0) REVERT: B 118 ASN cc_start: 0.8171 (t0) cc_final: 0.7955 (t160) REVERT: C 181 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8738 (ttpp) REVERT: D 8 ASN cc_start: 0.8777 (t0) cc_final: 0.8178 (t0) REVERT: E 27 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7956 (tptm) REVERT: I 75 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: I 156 ASP cc_start: 0.8987 (t0) cc_final: 0.8570 (t0) REVERT: J 118 ASN cc_start: 0.8173 (t0) cc_final: 0.7958 (t160) REVERT: L 8 ASN cc_start: 0.8768 (t0) cc_final: 0.8166 (t0) REVERT: M 27 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7954 (tptm) outliers start: 38 outliers final: 18 residues processed: 183 average time/residue: 0.8571 time to fit residues: 169.1132 Evaluate side-chains 176 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 27 LYS Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 41 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 23 optimal weight: 0.0070 chunk 138 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.072406 restraints weight = 33115.792| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.40 r_work: 0.2901 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 16728 Z= 0.131 Angle : 0.603 10.051 22864 Z= 0.281 Chirality : 0.043 0.150 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.568 82.557 2692 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.18 % Allowed : 9.93 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.61 (0.20), residues: 1940 helix: 2.68 (0.17), residues: 976 sheet: -0.05 (0.32), residues: 240 loop : -0.85 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 184 TYR 0.009 0.001 TYR I 105 PHE 0.011 0.001 PHE D 123 TRP 0.009 0.001 TRP I 146 HIS 0.006 0.001 HIS L 151 Details of bonding type rmsd covalent geometry : bond 0.00291 (16704) covalent geometry : angle 0.59711 (22854) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.74543 ( 4) hydrogen bonds : bond 0.07208 ( 805) hydrogen bonds : angle 3.75924 ( 2285) metal coordination : bond 0.00237 ( 8) metal coordination : angle 5.39529 ( 6) Misc. bond : bond 0.08441 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.681 Fit side-chains REVERT: A 75 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 131 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7025 (t80) REVERT: A 156 ASP cc_start: 0.8948 (t0) cc_final: 0.8538 (t0) REVERT: B 8 ASP cc_start: 0.8284 (t70) cc_final: 0.8040 (t70) REVERT: C 55 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7809 (mmt) REVERT: C 181 LYS cc_start: 0.9078 (ttpp) cc_final: 0.8736 (ttpp) REVERT: D 8 ASN cc_start: 0.8751 (t0) cc_final: 0.8155 (t0) REVERT: D 155 ASP cc_start: 0.5981 (OUTLIER) cc_final: 0.5432 (t70) REVERT: I 75 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: I 131 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7026 (t80) REVERT: I 156 ASP cc_start: 0.8950 (t0) cc_final: 0.8541 (t0) REVERT: J 8 ASP cc_start: 0.8288 (t70) cc_final: 0.8041 (t70) REVERT: L 8 ASN cc_start: 0.8748 (t0) cc_final: 0.8151 (t0) REVERT: L 155 ASP cc_start: 0.5984 (OUTLIER) cc_final: 0.5436 (t70) outliers start: 36 outliers final: 15 residues processed: 187 average time/residue: 0.8932 time to fit residues: 180.8147 Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 67 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 99 ASN J 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073189 restraints weight = 47609.151| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.86 r_work: 0.2904 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 16728 Z= 0.123 Angle : 0.588 9.063 22864 Z= 0.273 Chirality : 0.043 0.152 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.346 82.227 2692 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.00 % Allowed : 10.29 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.76 (0.20), residues: 1940 helix: 2.81 (0.17), residues: 976 sheet: 0.13 (0.34), residues: 220 loop : -0.81 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 184 TYR 0.007 0.001 TYR I 105 PHE 0.010 0.001 PHE I 131 TRP 0.008 0.001 TRP I 146 HIS 0.008 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00275 (16704) covalent geometry : angle 0.58123 (22854) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.68726 ( 4) hydrogen bonds : bond 0.06577 ( 805) hydrogen bonds : angle 3.63643 ( 2285) metal coordination : bond 0.00264 ( 8) metal coordination : angle 5.42392 ( 6) Misc. bond : bond 0.08030 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.727 Fit side-chains REVERT: A 75 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: A 131 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.6931 (t80) REVERT: A 156 ASP cc_start: 0.8955 (t0) cc_final: 0.8590 (t0) REVERT: C 181 LYS cc_start: 0.9076 (ttpp) cc_final: 0.8732 (ttpp) REVERT: D 8 ASN cc_start: 0.8749 (t0) cc_final: 0.8190 (t0) REVERT: D 155 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5402 (t70) REVERT: I 6 ASP cc_start: 0.8953 (m-30) cc_final: 0.8600 (m-30) REVERT: I 75 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: I 131 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.6932 (t80) REVERT: I 156 ASP cc_start: 0.8958 (t0) cc_final: 0.8592 (t0) REVERT: L 8 ASN cc_start: 0.8746 (t0) cc_final: 0.8185 (t0) REVERT: L 155 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.5428 (t70) outliers start: 33 outliers final: 14 residues processed: 197 average time/residue: 0.8436 time to fit residues: 179.8041 Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 3 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 121 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN L 121 ASN ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072310 restraints weight = 50129.875| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.89 r_work: 0.2886 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 16728 Z= 0.131 Angle : 0.607 9.167 22864 Z= 0.285 Chirality : 0.043 0.147 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.313 82.442 2692 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.33 % Allowed : 11.44 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.74 (0.20), residues: 1940 helix: 2.81 (0.17), residues: 976 sheet: 0.06 (0.32), residues: 240 loop : -0.84 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 184 TYR 0.009 0.001 TYR I 105 PHE 0.010 0.001 PHE A 52 TRP 0.008 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00299 (16704) covalent geometry : angle 0.60003 (22854) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.81690 ( 4) hydrogen bonds : bond 0.06832 ( 805) hydrogen bonds : angle 3.63399 ( 2285) metal coordination : bond 0.00255 ( 8) metal coordination : angle 5.55260 ( 6) Misc. bond : bond 0.08153 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.761 Fit side-chains REVERT: A 75 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: A 131 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7050 (t80) REVERT: A 156 ASP cc_start: 0.8969 (t0) cc_final: 0.8621 (t0) REVERT: C 181 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8730 (ttpp) REVERT: D 8 ASN cc_start: 0.8742 (t0) cc_final: 0.8153 (t0) REVERT: D 155 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5422 (t0) REVERT: I 6 ASP cc_start: 0.8949 (m-30) cc_final: 0.8560 (m-30) REVERT: I 75 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: I 131 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.7049 (t80) REVERT: I 156 ASP cc_start: 0.8971 (t0) cc_final: 0.8619 (t0) REVERT: L 8 ASN cc_start: 0.8749 (t0) cc_final: 0.8169 (t0) REVERT: L 155 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5470 (t0) outliers start: 22 outliers final: 9 residues processed: 179 average time/residue: 0.8994 time to fit residues: 173.7775 Evaluate side-chains 176 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 79 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 118 optimal weight: 0.0770 chunk 4 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.113594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.075895 restraints weight = 52417.633| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.98 r_work: 0.2960 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 16728 Z= 0.115 Angle : 0.575 8.576 22864 Z= 0.269 Chirality : 0.042 0.152 2552 Planarity : 0.005 0.068 2806 Dihedral : 9.959 81.381 2688 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.15 % Allowed : 11.38 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.92 (0.20), residues: 1940 helix: 2.96 (0.17), residues: 976 sheet: 0.24 (0.34), residues: 220 loop : -0.78 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 184 TYR 0.007 0.001 TYR B 80 PHE 0.010 0.001 PHE I 131 TRP 0.008 0.001 TRP A 118 HIS 0.004 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00260 (16704) covalent geometry : angle 0.56776 (22854) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.58689 ( 4) hydrogen bonds : bond 0.05493 ( 805) hydrogen bonds : angle 3.50797 ( 2285) metal coordination : bond 0.00279 ( 8) metal coordination : angle 5.69033 ( 6) Misc. bond : bond 0.06924 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.697 Fit side-chains REVERT: A 75 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: A 131 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 156 ASP cc_start: 0.8915 (t0) cc_final: 0.8579 (t0) REVERT: C 181 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8715 (ttpp) REVERT: D 8 ASN cc_start: 0.8743 (t0) cc_final: 0.8166 (t0) REVERT: D 140 ARG cc_start: 0.7777 (tmt170) cc_final: 0.7159 (tmt170) REVERT: D 155 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5381 (t70) REVERT: I 6 ASP cc_start: 0.8927 (m-30) cc_final: 0.8562 (m-30) REVERT: I 75 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7904 (mp0) REVERT: I 131 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7112 (t80) REVERT: I 156 ASP cc_start: 0.8921 (t0) cc_final: 0.8583 (t0) REVERT: L 8 ASN cc_start: 0.8742 (t0) cc_final: 0.8163 (t0) REVERT: L 140 ARG cc_start: 0.7772 (tmt170) cc_final: 0.7151 (tmt170) REVERT: L 155 ASP cc_start: 0.5871 (OUTLIER) cc_final: 0.5384 (t70) outliers start: 19 outliers final: 6 residues processed: 191 average time/residue: 0.8877 time to fit residues: 183.6968 Evaluate side-chains 180 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 17 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.067726 restraints weight = 38474.210| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.58 r_work: 0.2805 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.215 16728 Z= 0.199 Angle : 0.691 10.029 22864 Z= 0.326 Chirality : 0.047 0.144 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.670 83.796 2684 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.91 % Allowed : 12.23 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.49 (0.19), residues: 1940 helix: 2.54 (0.17), residues: 980 sheet: -0.02 (0.33), residues: 236 loop : -0.88 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 184 TYR 0.010 0.002 TYR I 105 PHE 0.015 0.002 PHE K 128 TRP 0.012 0.001 TRP L 164 HIS 0.008 0.001 HIS I 202 Details of bonding type rmsd covalent geometry : bond 0.00488 (16704) covalent geometry : angle 0.68429 (22854) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.29167 ( 4) hydrogen bonds : bond 0.09526 ( 805) hydrogen bonds : angle 3.86686 ( 2285) metal coordination : bond 0.00417 ( 8) metal coordination : angle 5.69443 ( 6) Misc. bond : bond 0.11937 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9406.59 seconds wall clock time: 159 minutes 57.45 seconds (9597.45 seconds total)