Starting phenix.real_space_refine on Tue Jan 21 04:44:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9es9_19940/01_2025/9es9_19940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9es9_19940/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9es9_19940/01_2025/9es9_19940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9es9_19940/01_2025/9es9_19940.map" model { file = "/net/cci-nas-00/data/ceres_data/9es9_19940/01_2025/9es9_19940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9es9_19940/01_2025/9es9_19940.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: K, O, P, I, J, L, M, N, 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: 11.83, per 1000 atoms: 0.72 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 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: 4.33 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.48 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: 5.11 Time building geometry restraints manager: 4.88 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: 9390 21.46 - 42.92: 323 42.92 - 64.38: 68 64.38 - 85.85: 24 85.85 - 107.31: 6 Dihedral angle restraints: 9811 sinusoidal: 4185 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 9808 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: 128 2.58 - 3.16: 13131 3.16 - 3.74: 22884 3.74 - 4.32: 34341 4.32 - 4.90: 57244 Nonbonded interactions: 127728 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=" SG CYS L 112 " pdb=" SG CYS L 127 " model vdw 2.033 3.760 ... (remaining 127723 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } 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 '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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 42.420 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.900 ------------------------------------------------------------------------------- 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 : 0.003 0.052 16704 Z= 0.223 Angle : 0.534 13.775 22854 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 : 3.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (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 TRP 0.008 0.001 TRP L 164 HIS 0.004 0.001 HIS A 202 PHE 0.011 0.001 PHE C 128 TYR 0.010 0.001 TYR I 136 ARG 0.003 0.000 ARG K 18 *********************** 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 : 1.828 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: 0.7848 (mm110) REVERT: L 8 ASN cc_start: 0.8746 (t0) cc_final: 0.8241 (t0) outliers start: 10 outliers final: 8 residues processed: 210 average time/residue: 1.7263 time to fit residues: 393.2342 Evaluate side-chains 177 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 54 ASP 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 157 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3598 r_free = 0.3598 target = 0.105439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.066422 restraints weight = 44853.913| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.78 r_work: 0.2768 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16704 Z= 0.316 Angle : 0.729 10.890 22854 Z= 0.352 Chirality : 0.048 0.172 2552 Planarity : 0.006 0.067 2806 Dihedral : 12.454 97.365 2702 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.03 % Allowed : 7.26 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.20), residues: 1940 helix: 2.19 (0.17), residues: 968 sheet: -0.12 (0.32), residues: 238 loop : -0.74 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.007 0.002 HIS I 202 PHE 0.016 0.002 PHE C 128 TYR 0.016 0.002 TYR I 136 ARG 0.008 0.001 ARG D 137 *********************** 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: 17 poor density : 167 time to evaluate : 1.807 Fit side-chains REVERT: A 156 ASP cc_start: 0.8981 (t0) cc_final: 0.8603 (t0) REVERT: C 181 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8750 (ttpp) REVERT: D 8 ASN cc_start: 0.8646 (t0) cc_final: 0.8103 (t0) REVERT: I 156 ASP cc_start: 0.8986 (t0) cc_final: 0.8608 (t0) REVERT: L 8 ASN cc_start: 0.8643 (t0) cc_final: 0.8095 (t0) REVERT: L 112 CYS cc_start: 0.8014 (m) cc_final: 0.7586 (p) outliers start: 17 outliers final: 6 residues processed: 177 average time/residue: 1.8519 time to fit residues: 353.8629 Evaluate side-chains 161 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 K 56 GLN L 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.070466 restraints weight = 50274.550| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.90 r_work: 0.2852 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16704 Z= 0.194 Angle : 0.599 9.185 22854 Z= 0.284 Chirality : 0.044 0.168 2552 Planarity : 0.005 0.067 2806 Dihedral : 10.992 83.727 2692 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.51 % Allowed : 8.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1940 helix: 2.52 (0.17), residues: 968 sheet: 0.00 (0.32), residues: 238 loop : -0.85 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 PHE 0.011 0.001 PHE A 52 TYR 0.008 0.001 TYR C 53 ARG 0.005 0.000 ARG K 50 *********************** 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 192 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.761 Fit side-chains REVERT: A 75 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 131 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 156 ASP cc_start: 0.8980 (t0) cc_final: 0.8564 (t0) REVERT: C 181 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8735 (ttpp) REVERT: D 8 ASN cc_start: 0.8704 (t0) cc_final: 0.8129 (t0) REVERT: E 27 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7948 (tptm) REVERT: I 75 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: I 131 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7003 (t80) REVERT: I 156 ASP cc_start: 0.8983 (t0) cc_final: 0.8566 (t0) REVERT: L 8 ASN cc_start: 0.8709 (t0) cc_final: 0.8138 (t0) REVERT: L 112 CYS cc_start: 0.7822 (m) cc_final: 0.7370 (p) REVERT: M 27 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7949 (tptm) REVERT: Q 50 GLU cc_start: 0.7707 (tt0) cc_final: 0.7471 (tt0) outliers start: 25 outliers final: 8 residues processed: 183 average time/residue: 1.8413 time to fit residues: 364.4305 Evaluate side-chains 166 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 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 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 54 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 121 optimal weight: 0.0980 chunk 162 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.067740 restraints weight = 41509.587| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.69 r_work: 0.2796 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 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 = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16704 Z= 0.272 Angle : 0.654 9.857 22854 Z= 0.309 Chirality : 0.046 0.156 2552 Planarity : 0.005 0.069 2806 Dihedral : 11.204 84.311 2692 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 9.14 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1940 helix: 2.47 (0.17), residues: 968 sheet: -0.06 (0.32), residues: 238 loop : -0.91 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 164 HIS 0.007 0.001 HIS A 202 PHE 0.015 0.002 PHE K 128 TYR 0.010 0.001 TYR K 146 ARG 0.005 0.001 ARG C 50 *********************** 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 191 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.696 Fit side-chains REVERT: A 75 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 156 ASP cc_start: 0.8981 (t0) cc_final: 0.8531 (t0) REVERT: C 181 LYS cc_start: 0.9118 (ttpp) cc_final: 0.8760 (ttpp) REVERT: D 8 ASN cc_start: 0.8754 (t0) cc_final: 0.8149 (t0) REVERT: I 75 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: I 156 ASP cc_start: 0.8981 (t0) cc_final: 0.8531 (t0) REVERT: L 8 ASN cc_start: 0.8755 (t0) cc_final: 0.8147 (t0) REVERT: M 27 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7999 (tptm) outliers start: 27 outliers final: 13 residues processed: 181 average time/residue: 1.8347 time to fit residues: 359.0392 Evaluate side-chains 169 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 140 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 K 56 GLN 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 = 0.109296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.070921 restraints weight = 47217.446| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.84 r_work: 0.2860 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16704 Z= 0.191 Angle : 0.592 9.064 22854 Z= 0.280 Chirality : 0.044 0.155 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.733 82.808 2692 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.00 % Allowed : 9.75 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1940 helix: 2.68 (0.17), residues: 966 sheet: -0.01 (0.32), residues: 240 loop : -0.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 146 HIS 0.005 0.001 HIS L 151 PHE 0.010 0.001 PHE D 123 TYR 0.009 0.001 TYR I 105 ARG 0.005 0.000 ARG K 184 *********************** 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 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.610 Fit side-chains REVERT: A 75 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: A 131 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.7073 (t80) REVERT: A 156 ASP cc_start: 0.8965 (t0) cc_final: 0.8528 (t0) REVERT: B 8 ASP cc_start: 0.8283 (t70) cc_final: 0.8018 (t70) REVERT: C 181 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8736 (ttpp) REVERT: D 8 ASN cc_start: 0.8757 (t0) cc_final: 0.8159 (t0) REVERT: I 75 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: I 131 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7066 (t80) REVERT: I 156 ASP cc_start: 0.8968 (t0) cc_final: 0.8529 (t0) REVERT: J 8 ASP cc_start: 0.8282 (t70) cc_final: 0.8014 (t70) REVERT: K 55 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7758 (mmt) REVERT: L 8 ASN cc_start: 0.8752 (t0) cc_final: 0.8153 (t0) outliers start: 33 outliers final: 17 residues processed: 189 average time/residue: 1.7459 time to fit residues: 359.6204 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 : 1.692 ------------------------------------------------------------------------------- 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 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 I residue 54 MET 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 55 MET Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain Q residue 38 LEU 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 159 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN K 99 ASN L 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071687 restraints weight = 43109.807| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.74 r_work: 0.2876 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16704 Z= 0.191 Angle : 0.592 9.299 22854 Z= 0.277 Chirality : 0.043 0.150 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.568 82.718 2692 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.12 % Allowed : 10.35 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1940 helix: 2.78 (0.17), residues: 964 sheet: 0.02 (0.32), residues: 240 loop : -0.87 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 118 HIS 0.006 0.001 HIS D 151 PHE 0.011 0.001 PHE A 52 TYR 0.009 0.001 TYR I 105 ARG 0.007 0.000 ARG K 184 *********************** 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 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.900 Fit side-chains REVERT: A 75 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: A 131 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.7067 (t80) REVERT: A 156 ASP cc_start: 0.8973 (t0) cc_final: 0.8549 (t0) REVERT: B 8 ASP cc_start: 0.8290 (t70) cc_final: 0.8045 (t70) REVERT: C 99 ASN cc_start: 0.8070 (t0) cc_final: 0.7867 (t0) REVERT: C 181 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8738 (ttpp) REVERT: D 8 ASN cc_start: 0.8770 (t0) cc_final: 0.8181 (t0) REVERT: D 155 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5426 (t70) REVERT: E 27 LYS cc_start: 0.8224 (tptm) cc_final: 0.7998 (tppt) REVERT: I 75 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: I 131 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.7061 (t80) REVERT: I 156 ASP cc_start: 0.8975 (t0) cc_final: 0.8548 (t0) REVERT: J 8 ASP cc_start: 0.8304 (t70) cc_final: 0.8050 (t70) REVERT: L 8 ASN cc_start: 0.8770 (t0) cc_final: 0.8181 (t0) REVERT: L 155 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5450 (t70) outliers start: 35 outliers final: 17 residues processed: 187 average time/residue: 1.6949 time to fit residues: 344.5089 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 A residue 163 SER Chi-restraints excluded: chain B residue 35 ASP 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 D residue 97 THR Chi-restraints excluded: chain D residue 155 ASP 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 I residue 163 SER Chi-restraints excluded: chain J residue 35 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 170 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.070198 restraints weight = 45759.387| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.81 r_work: 0.2844 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16704 Z= 0.215 Angle : 0.607 9.552 22854 Z= 0.286 Chirality : 0.044 0.148 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.598 83.282 2692 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.00 % Allowed : 10.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1940 helix: 2.70 (0.17), residues: 974 sheet: -0.03 (0.32), residues: 240 loop : -0.86 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 164 HIS 0.006 0.001 HIS D 151 PHE 0.011 0.001 PHE C 128 TYR 0.009 0.001 TYR A 105 ARG 0.006 0.000 ARG K 184 *********************** 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 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.835 Fit side-chains REVERT: A 75 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: A 131 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.7066 (t80) REVERT: A 156 ASP cc_start: 0.8958 (t0) cc_final: 0.8554 (t0) REVERT: B 8 ASP cc_start: 0.8273 (t70) cc_final: 0.8040 (t70) REVERT: C 99 ASN cc_start: 0.8139 (t0) cc_final: 0.7936 (t0) REVERT: C 181 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8717 (ttpp) REVERT: D 8 ASN cc_start: 0.8761 (t0) cc_final: 0.8169 (t0) REVERT: D 155 ASP cc_start: 0.5965 (OUTLIER) cc_final: 0.5423 (t70) REVERT: E 27 LYS cc_start: 0.8221 (tptm) cc_final: 0.8001 (tppt) REVERT: I 75 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: I 131 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.7059 (t80) REVERT: I 156 ASP cc_start: 0.8957 (t0) cc_final: 0.8552 (t0) REVERT: J 8 ASP cc_start: 0.8262 (t70) cc_final: 0.8026 (t70) REVERT: L 8 ASN cc_start: 0.8775 (t0) cc_final: 0.8182 (t0) REVERT: L 155 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5434 (t70) REVERT: M 27 LYS cc_start: 0.8217 (tptm) cc_final: 0.7997 (tppt) outliers start: 33 outliers final: 16 residues processed: 189 average time/residue: 1.6852 time to fit residues: 347.3658 Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 35 ASP 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 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 35 ASP 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 N residue 34 VAL 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 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN J 118 ASN L 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.071755 restraints weight = 36540.550| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.53 r_work: 0.2880 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16704 Z= 0.197 Angle : 0.601 10.420 22854 Z= 0.283 Chirality : 0.044 0.149 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.470 82.849 2692 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.06 % Allowed : 10.65 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.20), residues: 1940 helix: 2.74 (0.17), residues: 976 sheet: 0.10 (0.34), residues: 220 loop : -0.81 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 146 HIS 0.007 0.001 HIS D 151 PHE 0.011 0.001 PHE I 52 TYR 0.009 0.001 TYR I 105 ARG 0.007 0.000 ARG K 184 *********************** 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 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 2.023 Fit side-chains REVERT: A 75 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 131 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7030 (t80) REVERT: A 156 ASP cc_start: 0.8949 (t0) cc_final: 0.8565 (t0) REVERT: B 8 ASP cc_start: 0.8275 (t70) cc_final: 0.8049 (t70) REVERT: C 99 ASN cc_start: 0.8129 (t0) cc_final: 0.7929 (t0) REVERT: C 181 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8730 (ttpp) REVERT: D 8 ASN cc_start: 0.8745 (t0) cc_final: 0.8178 (t0) REVERT: D 155 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5365 (t70) REVERT: E 27 LYS cc_start: 0.8192 (tptm) cc_final: 0.7976 (tppt) REVERT: I 75 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: I 131 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.7027 (t80) REVERT: I 156 ASP cc_start: 0.8948 (t0) cc_final: 0.8565 (t0) REVERT: J 8 ASP cc_start: 0.8272 (t70) cc_final: 0.8044 (t70) REVERT: L 8 ASN cc_start: 0.8751 (t0) cc_final: 0.8190 (t0) REVERT: L 155 ASP cc_start: 0.5985 (OUTLIER) cc_final: 0.5396 (t70) REVERT: M 27 LYS cc_start: 0.8189 (tptm) cc_final: 0.7970 (tppt) outliers start: 34 outliers final: 13 residues processed: 190 average time/residue: 1.6318 time to fit residues: 338.6082 Evaluate side-chains 180 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 35 ASP 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 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 J residue 35 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 100 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.109909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.071976 restraints weight = 42789.115| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.72 r_work: 0.2879 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16704 Z= 0.193 Angle : 0.600 9.237 22854 Z= 0.284 Chirality : 0.044 0.148 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.379 82.704 2692 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.39 % Allowed : 11.26 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.20), residues: 1940 helix: 2.77 (0.17), residues: 978 sheet: 0.15 (0.34), residues: 220 loop : -0.79 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.011 0.001 PHE A 52 TYR 0.009 0.001 TYR A 105 ARG 0.008 0.000 ARG K 184 *********************** 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 190 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.837 Fit side-chains REVERT: A 75 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: A 131 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7063 (t80) REVERT: A 156 ASP cc_start: 0.8965 (t0) cc_final: 0.8613 (t0) REVERT: C 99 ASN cc_start: 0.8197 (t0) cc_final: 0.7909 (t0) REVERT: D 8 ASN cc_start: 0.8747 (t0) cc_final: 0.8174 (t0) REVERT: E 27 LYS cc_start: 0.8110 (tptm) cc_final: 0.7907 (tppt) REVERT: I 6 ASP cc_start: 0.8957 (m-30) cc_final: 0.8565 (m-30) REVERT: I 75 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: I 131 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7061 (t80) REVERT: I 156 ASP cc_start: 0.8963 (t0) cc_final: 0.8610 (t0) REVERT: L 8 ASN cc_start: 0.8758 (t0) cc_final: 0.8188 (t0) REVERT: M 27 LYS cc_start: 0.8123 (tptm) cc_final: 0.7913 (tppt) outliers start: 23 outliers final: 15 residues processed: 182 average time/residue: 1.7246 time to fit residues: 340.5814 Evaluate side-chains 181 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 35 ASP 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 D residue 97 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 35 ASP 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 R residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 82 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 32 optimal weight: 0.0060 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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 121 ASN ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.108528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069745 restraints weight = 52985.331| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.96 r_work: 0.2829 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 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 = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16704 Z= 0.226 Angle : 0.632 9.440 22854 Z= 0.299 Chirality : 0.044 0.146 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.493 83.369 2692 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.57 % Allowed : 11.50 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.20), residues: 1940 helix: 2.69 (0.17), residues: 978 sheet: 0.00 (0.32), residues: 240 loop : -0.84 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 164 HIS 0.006 0.001 HIS A 202 PHE 0.012 0.001 PHE C 128 TYR 0.009 0.001 TYR I 105 ARG 0.009 0.000 ARG K 184 ********************** 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 189 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.819 Fit side-chains REVERT: A 75 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: A 156 ASP cc_start: 0.8975 (t0) cc_final: 0.8618 (t0) REVERT: C 99 ASN cc_start: 0.8307 (t0) cc_final: 0.8037 (t0) REVERT: C 181 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8285 (ptmm) REVERT: D 8 ASN cc_start: 0.8759 (t0) cc_final: 0.8168 (t0) REVERT: D 140 ARG cc_start: 0.7804 (tmt170) cc_final: 0.7164 (tmt170) REVERT: E 27 LYS cc_start: 0.8215 (tptm) cc_final: 0.7994 (tppt) REVERT: I 6 ASP cc_start: 0.8966 (m-30) cc_final: 0.8590 (m-30) REVERT: I 75 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: I 156 ASP cc_start: 0.8972 (t0) cc_final: 0.8614 (t0) REVERT: L 8 ASN cc_start: 0.8781 (t0) cc_final: 0.8196 (t0) REVERT: M 27 LYS cc_start: 0.8219 (tptm) cc_final: 0.7996 (tppt) outliers start: 26 outliers final: 14 residues processed: 179 average time/residue: 1.7344 time to fit residues: 337.8696 Evaluate side-chains 178 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 35 ASP 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 97 THR Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain N residue 34 VAL 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 67 optimal weight: 0.0770 chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 148 optimal weight: 0.0770 chunk 152 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074629 restraints weight = 39382.874| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.58 r_work: 0.2940 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16704 Z= 0.174 Angle : 0.579 8.422 22854 Z= 0.275 Chirality : 0.043 0.151 2552 Planarity : 0.005 0.068 2806 Dihedral : 10.058 81.887 2684 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.03 % Allowed : 11.92 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.20), residues: 1940 helix: 2.86 (0.17), residues: 978 sheet: 0.18 (0.34), residues: 220 loop : -0.78 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.010 0.001 PHE A 198 TYR 0.007 0.001 TYR J 80 ARG 0.009 0.000 ARG C 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18043.20 seconds wall clock time: 316 minutes 47.88 seconds (19007.88 seconds total)