Starting phenix.real_space_refine on Sat Jun 14 16:00:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9es9_19940/06_2025/9es9_19940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9es9_19940/06_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_19940/06_2025/9es9_19940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9es9_19940/06_2025/9es9_19940.map" model { file = "/net/cci-nas-00/data/ceres_data/9es9_19940/06_2025/9es9_19940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9es9_19940/06_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-5710/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: 11.85, 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=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.1 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: 1.72 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: 4.59 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6358 1.39 - 1.59: 10180 1.59 - 1.79: 46 1.79 - 2.00: 72 2.00 - 2.20: 48 Bond restraints: 16704 Sorted by residual: bond pdb=" N GLY J 2 " pdb=" CA GLY J 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N LYS Q 32 " pdb=" CA LYS Q 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N LYS R 32 " pdb=" CA LYS R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 16699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 22683 2.76 - 5.51: 167 5.51 - 8.27: 2 8.27 - 11.02: 0 11.02 - 13.78: 2 Bond angle restraints: 22854 Sorted by residual: angle pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sigma weight residual 109.00 122.78 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sigma weight residual 109.00 122.78 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C GLN C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.83 125.21 -3.38 1.56e+00 4.11e-01 4.69e+00 angle pdb=" C GLN K 246 " pdb=" N ASP K 247 " pdb=" CA ASP K 247 " ideal model delta sigma weight residual 121.83 125.14 -3.31 1.56e+00 4.11e-01 4.51e+00 angle pdb=" CA GLY L 102 " pdb=" C GLY L 102 " pdb=" N ILE L 103 " ideal model delta sigma weight residual 114.75 117.71 -2.96 1.40e+00 5.10e-01 4.47e+00 ... (remaining 22849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 9393 21.46 - 42.92: 323 42.92 - 64.38: 68 64.38 - 85.85: 24 85.85 - 107.31: 6 Dihedral angle restraints: 9814 sinusoidal: 4188 harmonic: 5626 Sorted by residual: dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 8.21 51.79 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2C HEC I 303 " pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sinusoidal sigma weight residual 60.00 8.21 51.79 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2B HEC I 303 " pdb=" C3B HEC I 303 " pdb=" CAB HEC I 303 " pdb=" CBB HEC I 303 " ideal model delta sinusoidal sigma weight residual -120.00 -74.11 -45.89 2 1.00e+01 1.00e-02 2.47e+01 ... (remaining 9811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1441 0.027 - 0.053: 677 0.053 - 0.080: 238 0.080 - 0.107: 116 0.107 - 0.133: 80 Chirality restraints: 2552 Sorted by residual: chirality pdb=" CA ILE G 2 " pdb=" N ILE G 2 " pdb=" C ILE G 2 " pdb=" CB ILE G 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE O 2 " pdb=" N ILE O 2 " pdb=" C ILE O 2 " pdb=" CB ILE O 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE K 51 " pdb=" N ILE K 51 " pdb=" C ILE K 51 " pdb=" CB ILE K 51 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2549 not shown) Planarity restraints: 2806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 162 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO L 163 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 163 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 163 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 162 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO D 163 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 146 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO K 147 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO K 147 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 147 " 0.020 5.00e-02 4.00e+02 ... (remaining 2803 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 127 2.58 - 3.16: 13129 3.16 - 3.74: 22884 3.74 - 4.32: 34341 4.32 - 4.90: 57244 Nonbonded interactions: 127725 Sorted by model distance: nonbonded pdb=" OD2 ASP B 35 " pdb=" O HOH B 301 " model vdw 1.994 3.040 nonbonded pdb=" OD2 ASP J 35 " pdb=" O HOH J 301 " model vdw 1.996 3.040 nonbonded pdb=" OD1 ASP J 35 " pdb=" O HOH J 302 " model vdw 2.022 3.040 nonbonded pdb=" OD1 ASP B 35 " pdb=" O HOH B 302 " model vdw 2.023 3.040 nonbonded pdb=" O HOH K 413 " pdb=" O HOH K 422 " model vdw 2.067 3.040 ... (remaining 127720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.000 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.737 16728 Z= 0.273 Angle : 0.543 13.775 22864 Z= 0.243 Chirality : 0.042 0.133 2552 Planarity : 0.004 0.061 2806 Dihedral : 12.293 107.306 6204 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.25 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 Details of bonding type rmsd hydrogen bonds : bond 0.31861 ( 805) hydrogen bonds : angle 6.36779 ( 2285) metal coordination : bond 0.02083 ( 8) metal coordination : angle 6.29373 ( 6) SS BOND : bond 0.00178 ( 2) SS BOND : angle 1.16426 ( 4) covalent geometry : bond 0.00349 (16704) covalent geometry : angle 0.53369 (22854) Misc. bond : bond 0.35219 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.730 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: 1.7182 time to fit residues: 391.9424 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 : 1.783 ------------------------------------------------------------------------------- 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: 3.9990 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 = 0.105438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066428 restraints weight = 44932.728| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.78 r_work: 0.2767 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 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 = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 16728 Z= 0.208 Angle : 0.724 10.890 22864 Z= 0.346 Chirality : 0.048 0.170 2552 Planarity : 0.005 0.067 2806 Dihedral : 12.446 95.319 2702 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.03 % Allowed : 7.08 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.20), residues: 1940 helix: 2.16 (0.17), residues: 968 sheet: -0.12 (0.32), residues: 238 loop : -0.73 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 146 HIS 0.008 0.002 HIS I 202 PHE 0.016 0.002 PHE C 128 TYR 0.016 0.002 TYR I 136 ARG 0.007 0.001 ARG K 50 Details of bonding type rmsd hydrogen bonds : bond 0.11380 ( 805) hydrogen bonds : angle 4.39944 ( 2285) metal coordination : bond 0.00568 ( 8) metal coordination : angle 5.98711 ( 6) SS BOND : bond 0.00183 ( 2) SS BOND : angle 1.33574 ( 4) covalent geometry : bond 0.00487 (16704) covalent geometry : angle 0.71694 (22854) Misc. bond : bond 0.12365 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 1.633 Fit side-chains REVERT: A 156 ASP cc_start: 0.8976 (t0) cc_final: 0.8601 (t0) REVERT: C 181 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8755 (ttpp) REVERT: D 8 ASN cc_start: 0.8652 (t0) cc_final: 0.8107 (t0) REVERT: I 156 ASP cc_start: 0.8981 (t0) cc_final: 0.8605 (t0) REVERT: L 8 ASN cc_start: 0.8651 (t0) cc_final: 0.8102 (t0) outliers start: 17 outliers final: 6 residues processed: 178 average time/residue: 1.8046 time to fit residues: 348.0196 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 : 1.712 ------------------------------------------------------------------------------- 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: 0.9980 chunk 128 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.110007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.071589 restraints weight = 50274.386| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.92 r_work: 0.2871 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 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 = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.191 16728 Z= 0.135 Angle : 0.598 9.058 22864 Z= 0.281 Chirality : 0.044 0.165 2552 Planarity : 0.005 0.067 2806 Dihedral : 10.919 83.604 2692 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.45 % Allowed : 8.11 % Favored : 90.44 % 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: 1.52 (0.20), residues: 1940 helix: 2.55 (0.17), residues: 968 sheet: 0.11 (0.34), residues: 218 loop : -0.80 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 146 HIS 0.004 0.001 HIS D 151 PHE 0.011 0.001 PHE A 52 TYR 0.007 0.001 TYR C 53 ARG 0.005 0.000 ARG K 50 Details of bonding type rmsd hydrogen bonds : bond 0.07727 ( 805) hydrogen bonds : angle 3.94670 ( 2285) metal coordination : bond 0.00298 ( 8) metal coordination : angle 5.83469 ( 6) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.72933 ( 4) covalent geometry : bond 0.00285 (16704) covalent geometry : angle 0.59080 (22854) Misc. bond : bond 0.08431 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.951 Fit side-chains REVERT: A 75 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 131 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.7054 (t80) REVERT: A 156 ASP cc_start: 0.8978 (t0) cc_final: 0.8565 (t0) REVERT: C 181 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8772 (ttpp) REVERT: D 8 ASN cc_start: 0.8741 (t0) cc_final: 0.8175 (t0) REVERT: E 27 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7940 (tptm) REVERT: I 75 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: I 131 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.7048 (t80) REVERT: I 156 ASP cc_start: 0.8978 (t0) cc_final: 0.8564 (t0) REVERT: L 8 ASN cc_start: 0.8737 (t0) cc_final: 0.8167 (t0) REVERT: M 27 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7946 (tptm) REVERT: Q 50 GLU cc_start: 0.7693 (tt0) cc_final: 0.7442 (tt0) outliers start: 24 outliers final: 8 residues processed: 182 average time/residue: 1.7955 time to fit residues: 354.5190 Evaluate side-chains 167 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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: 0.0670 chunk 151 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 163 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 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 = 0.3652 r_free = 0.3652 target = 0.109528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.071385 restraints weight = 42542.185| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.72 r_work: 0.2873 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- 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: 0.8691 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 16728 Z= 0.137 Angle : 0.599 9.546 22864 Z= 0.278 Chirality : 0.044 0.160 2552 Planarity : 0.005 0.068 2806 Dihedral : 10.821 83.498 2692 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.88 % Allowed : 8.54 % Favored : 89.59 % 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: 1.60 (0.20), residues: 1940 helix: 2.65 (0.17), residues: 968 sheet: 0.12 (0.32), residues: 238 loop : -0.85 (0.22), residues: 734 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 I 52 TYR 0.009 0.001 TYR A 105 ARG 0.006 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.07656 ( 805) hydrogen bonds : angle 3.83005 ( 2285) metal coordination : bond 0.00365 ( 8) metal coordination : angle 5.67123 ( 6) SS BOND : bond 0.00153 ( 2) SS BOND : angle 0.88287 ( 4) covalent geometry : bond 0.00304 (16704) covalent geometry : angle 0.59227 (22854) Misc. bond : bond 0.08708 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.795 Fit side-chains REVERT: A 75 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: A 131 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7015 (t80) REVERT: A 156 ASP cc_start: 0.8988 (t0) cc_final: 0.8531 (t0) REVERT: B 8 ASP cc_start: 0.8296 (t70) cc_final: 0.8009 (t70) REVERT: C 181 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8758 (ttpp) REVERT: D 8 ASN cc_start: 0.8726 (t0) cc_final: 0.8171 (t0) REVERT: I 75 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: I 131 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7014 (t80) REVERT: I 156 ASP cc_start: 0.8992 (t0) cc_final: 0.8537 (t0) REVERT: J 8 ASP cc_start: 0.8275 (t70) cc_final: 0.7990 (t70) REVERT: L 8 ASN cc_start: 0.8731 (t0) cc_final: 0.8172 (t0) outliers start: 31 outliers final: 11 residues processed: 186 average time/residue: 1.7558 time to fit residues: 353.5399 Evaluate side-chains 170 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 17 LYS 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 I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 17 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 140 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN C 99 ASN K 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.069656 restraints weight = 47382.736| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.85 r_work: 0.2833 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 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 = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 16728 Z= 0.151 Angle : 0.622 9.521 22864 Z= 0.289 Chirality : 0.044 0.154 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.821 83.829 2692 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.88 % Allowed : 9.93 % Favored : 88.20 % 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 (0.19), residues: 1940 helix: 2.65 (0.17), residues: 968 sheet: 0.08 (0.32), residues: 238 loop : -0.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 164 HIS 0.007 0.001 HIS I 202 PHE 0.012 0.001 PHE C 128 TYR 0.009 0.001 TYR I 105 ARG 0.006 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.08217 ( 805) hydrogen bonds : angle 3.83719 ( 2285) metal coordination : bond 0.00361 ( 8) metal coordination : angle 5.59876 ( 6) SS BOND : bond 0.00180 ( 2) SS BOND : angle 1.06651 ( 4) covalent geometry : bond 0.00353 (16704) covalent geometry : angle 0.61578 (22854) Misc. bond : bond 0.09235 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.623 Fit side-chains REVERT: A 75 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: A 156 ASP cc_start: 0.8969 (t0) cc_final: 0.8527 (t0) REVERT: B 8 ASP cc_start: 0.8276 (t70) cc_final: 0.7997 (t70) REVERT: B 118 ASN cc_start: 0.8143 (t0) cc_final: 0.7937 (t160) REVERT: C 181 LYS cc_start: 0.9115 (ttpp) cc_final: 0.8758 (ttpp) REVERT: D 8 ASN cc_start: 0.8745 (t0) cc_final: 0.8170 (t0) REVERT: D 12 MET cc_start: 0.7681 (mmt) cc_final: 0.7443 (mmt) REVERT: I 75 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: I 156 ASP cc_start: 0.8969 (t0) cc_final: 0.8526 (t0) REVERT: J 8 ASP cc_start: 0.8293 (t70) cc_final: 0.8009 (t70) REVERT: J 118 ASN cc_start: 0.8150 (t0) cc_final: 0.7936 (t160) REVERT: L 8 ASN cc_start: 0.8748 (t0) cc_final: 0.8169 (t0) REVERT: L 12 MET cc_start: 0.7673 (mmt) cc_final: 0.7438 (mmt) outliers start: 31 outliers final: 15 residues processed: 184 average time/residue: 1.6707 time to fit residues: 333.8119 Evaluate side-chains 172 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain 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: 8.9990 chunk 176 optimal weight: 0.5980 chunk 185 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070651 restraints weight = 43083.737| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.70 r_work: 0.2856 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 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 = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.185 16728 Z= 0.141 Angle : 0.607 9.275 22864 Z= 0.282 Chirality : 0.044 0.152 2552 Planarity : 0.005 0.070 2806 Dihedral : 10.655 83.308 2692 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.24 % Allowed : 9.99 % Favored : 87.77 % 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: 1.60 (0.19), residues: 1940 helix: 2.71 (0.17), residues: 966 sheet: 0.01 (0.32), residues: 240 loop : -0.87 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 164 HIS 0.006 0.001 HIS A 202 PHE 0.011 0.001 PHE D 123 TYR 0.010 0.001 TYR I 105 ARG 0.007 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.07795 ( 805) hydrogen bonds : angle 3.78212 ( 2285) metal coordination : bond 0.00305 ( 8) metal coordination : angle 5.54626 ( 6) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.94960 ( 4) covalent geometry : bond 0.00325 (16704) covalent geometry : angle 0.60051 (22854) Misc. bond : bond 0.08982 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 1.749 Fit side-chains REVERT: A 75 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: A 131 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7070 (t80) REVERT: A 156 ASP cc_start: 0.8961 (t0) cc_final: 0.8532 (t0) REVERT: B 8 ASP cc_start: 0.8308 (t70) cc_final: 0.8044 (t70) REVERT: C 181 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8736 (ttpp) REVERT: D 8 ASN cc_start: 0.8758 (t0) cc_final: 0.8161 (t0) REVERT: D 12 MET cc_start: 0.7706 (mmt) cc_final: 0.7483 (mmt) REVERT: D 155 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5470 (t70) REVERT: E 27 LYS cc_start: 0.8223 (tptm) cc_final: 0.7998 (tppt) REVERT: I 75 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: I 131 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.7069 (t80) REVERT: I 156 ASP cc_start: 0.8962 (t0) cc_final: 0.8532 (t0) REVERT: J 8 ASP cc_start: 0.8304 (t70) cc_final: 0.8036 (t70) REVERT: J 118 ASN cc_start: 0.8160 (t0) cc_final: 0.7947 (t160) REVERT: L 8 ASN cc_start: 0.8755 (t0) cc_final: 0.8156 (t0) REVERT: L 12 MET cc_start: 0.7691 (mmt) cc_final: 0.7483 (mmt) REVERT: L 155 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5485 (t70) outliers start: 37 outliers final: 14 residues processed: 189 average time/residue: 1.6657 time to fit residues: 342.5820 Evaluate side-chains 176 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain 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: 6.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 171 optimal weight: 0.0270 chunk 111 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 140 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.7446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.110141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.072118 restraints weight = 45871.807| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.76 r_work: 0.2886 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 16728 Z= 0.129 Angle : 0.593 10.930 22864 Z= 0.275 Chirality : 0.043 0.150 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.463 82.781 2692 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.06 % Allowed : 10.41 % 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: 1.72 (0.20), residues: 1940 helix: 2.75 (0.17), residues: 976 sheet: 0.14 (0.34), residues: 220 loop : -0.79 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 146 HIS 0.007 0.001 HIS L 151 PHE 0.010 0.001 PHE A 52 TYR 0.009 0.001 TYR A 105 ARG 0.006 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.07079 ( 805) hydrogen bonds : angle 3.69653 ( 2285) metal coordination : bond 0.00312 ( 8) metal coordination : angle 5.53151 ( 6) SS BOND : bond 0.00123 ( 2) SS BOND : angle 0.80146 ( 4) covalent geometry : bond 0.00290 (16704) covalent geometry : angle 0.58607 (22854) Misc. bond : bond 0.08343 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.976 Fit side-chains REVERT: A 75 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 131 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 156 ASP cc_start: 0.8958 (t0) cc_final: 0.8539 (t0) REVERT: B 8 ASP cc_start: 0.8250 (t70) cc_final: 0.8037 (t70) REVERT: C 181 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8755 (ttpp) REVERT: D 8 ASN cc_start: 0.8763 (t0) cc_final: 0.8198 (t0) REVERT: D 155 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.5431 (t70) REVERT: E 27 LYS cc_start: 0.8113 (tptm) cc_final: 0.7900 (tppt) REVERT: G 31 ARG cc_start: 0.6811 (mtm-85) cc_final: 0.6588 (mtm-85) REVERT: I 75 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: I 131 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.6948 (t80) REVERT: I 156 ASP cc_start: 0.8960 (t0) cc_final: 0.8541 (t0) REVERT: J 8 ASP cc_start: 0.8249 (t70) cc_final: 0.8032 (t70) REVERT: L 8 ASN cc_start: 0.8764 (t0) cc_final: 0.8196 (t0) REVERT: L 151 HIS cc_start: 0.7957 (t70) cc_final: 0.7706 (t-90) REVERT: L 155 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5446 (t70) REVERT: M 27 LYS cc_start: 0.8151 (tptm) cc_final: 0.7929 (tppt) outliers start: 34 outliers final: 16 residues processed: 195 average time/residue: 1.7797 time to fit residues: 378.0707 Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 155 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 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: 0.9980 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3652 r_free = 0.3652 target = 0.109411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.071758 restraints weight = 36672.808| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.50 r_work: 0.2882 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 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 = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 16728 Z= 0.139 Angle : 0.613 9.380 22864 Z= 0.285 Chirality : 0.044 0.146 2552 Planarity : 0.005 0.070 2806 Dihedral : 10.473 83.079 2692 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.00 % Allowed : 10.71 % 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: 0.05 (0.32), residues: 240 loop : -0.83 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 164 HIS 0.007 0.001 HIS L 151 PHE 0.011 0.001 PHE C 128 TYR 0.010 0.001 TYR I 105 ARG 0.007 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.07454 ( 805) hydrogen bonds : angle 3.70054 ( 2285) metal coordination : bond 0.00261 ( 8) metal coordination : angle 5.55651 ( 6) SS BOND : bond 0.00156 ( 2) SS BOND : angle 0.90965 ( 4) covalent geometry : bond 0.00320 (16704) covalent geometry : angle 0.60659 (22854) Misc. bond : bond 0.08705 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 2.641 Fit side-chains REVERT: A 75 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.7924 (mp0) REVERT: A 131 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 156 ASP cc_start: 0.8952 (t0) cc_final: 0.8566 (t0) REVERT: B 8 ASP cc_start: 0.8280 (t70) cc_final: 0.8063 (t70) REVERT: C 181 LYS cc_start: 0.9064 (ttpp) cc_final: 0.8724 (ttpp) REVERT: D 8 ASN cc_start: 0.8758 (t0) cc_final: 0.8199 (t0) REVERT: D 155 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5375 (t70) REVERT: E 27 LYS cc_start: 0.8207 (tptm) cc_final: 0.7990 (tppt) REVERT: G 31 ARG cc_start: 0.6924 (mtm-85) cc_final: 0.6709 (mtm-85) REVERT: I 6 ASP cc_start: 0.8941 (m-30) cc_final: 0.8527 (m-30) REVERT: I 75 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: I 131 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7052 (t80) REVERT: I 156 ASP cc_start: 0.8954 (t0) cc_final: 0.8567 (t0) REVERT: J 8 ASP cc_start: 0.8278 (t70) cc_final: 0.8056 (t70) REVERT: L 8 ASN cc_start: 0.8759 (t0) cc_final: 0.8197 (t0) REVERT: L 151 HIS cc_start: 0.7858 (t70) cc_final: 0.7575 (t-90) REVERT: L 155 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5377 (t70) REVERT: M 27 LYS cc_start: 0.8207 (tptm) cc_final: 0.7983 (tppt) outliers start: 33 outliers final: 16 residues processed: 188 average time/residue: 1.7149 time to fit residues: 351.7721 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.985 ------------------------------------------------------------------------------- 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 205 MET 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 155 ASP Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 205 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 100 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.0570 chunk 2 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074460 restraints weight = 43050.340| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.71 r_work: 0.2932 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 16728 Z= 0.121 Angle : 0.581 8.633 22864 Z= 0.272 Chirality : 0.043 0.149 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.190 82.051 2692 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.15 % Allowed : 11.32 % 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: 1.86 (0.20), residues: 1940 helix: 2.88 (0.17), residues: 976 sheet: 0.19 (0.34), residues: 220 loop : -0.75 (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 0.010 0.001 PHE I 131 TYR 0.007 0.001 TYR B 80 ARG 0.008 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.06163 ( 805) hydrogen bonds : angle 3.58204 ( 2285) metal coordination : bond 0.00301 ( 8) metal coordination : angle 5.58937 ( 6) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.67055 ( 4) covalent geometry : bond 0.00271 (16704) covalent geometry : angle 0.57440 (22854) Misc. bond : bond 0.07583 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.813 Fit side-chains REVERT: A 75 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: A 131 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.6992 (t80) REVERT: A 156 ASP cc_start: 0.8918 (t0) cc_final: 0.8569 (t0) REVERT: C 181 LYS cc_start: 0.9068 (ttpp) cc_final: 0.8738 (ttpp) REVERT: D 8 ASN cc_start: 0.8755 (t0) cc_final: 0.8206 (t0) REVERT: I 6 ASP cc_start: 0.8938 (m-30) cc_final: 0.8563 (m-30) REVERT: I 75 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: I 131 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.6989 (t80) REVERT: I 156 ASP cc_start: 0.8922 (t0) cc_final: 0.8571 (t0) REVERT: L 8 ASN cc_start: 0.8754 (t0) cc_final: 0.8196 (t0) outliers start: 19 outliers final: 12 residues processed: 181 average time/residue: 1.7676 time to fit residues: 348.5091 Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 205 MET 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 F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 205 MET 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 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: 3.9990 chunk 163 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 159 optimal weight: 0.0970 chunk 174 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN L 121 ASN N 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.108193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.069286 restraints weight = 53190.806| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.00 r_work: 0.2824 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 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 = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 16728 Z= 0.161 Angle : 0.647 9.523 22864 Z= 0.303 Chirality : 0.045 0.147 2552 Planarity : 0.005 0.070 2806 Dihedral : 10.448 83.650 2684 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.39 % Allowed : 11.68 % 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: 1.68 (0.20), residues: 1940 helix: 2.73 (0.17), residues: 976 sheet: 0.07 (0.32), residues: 240 loop : -0.84 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 164 HIS 0.008 0.001 HIS L 151 PHE 0.013 0.002 PHE C 128 TYR 0.009 0.001 TYR I 105 ARG 0.009 0.001 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.08202 ( 805) hydrogen bonds : angle 3.73178 ( 2285) metal coordination : bond 0.00322 ( 8) metal coordination : angle 5.57408 ( 6) SS BOND : bond 0.00186 ( 2) SS BOND : angle 1.08860 ( 4) covalent geometry : bond 0.00386 (16704) covalent geometry : angle 0.64020 (22854) Misc. bond : bond 0.09779 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.681 Fit side-chains REVERT: A 75 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: A 156 ASP cc_start: 0.8974 (t0) cc_final: 0.8625 (t0) REVERT: B 118 ASN cc_start: 0.8152 (t0) cc_final: 0.7950 (t160) REVERT: C 181 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8699 (ttpp) REVERT: D 8 ASN cc_start: 0.8755 (t0) cc_final: 0.8179 (t0) REVERT: D 140 ARG cc_start: 0.7843 (tmt170) cc_final: 0.7176 (tmt170) REVERT: I 6 ASP cc_start: 0.8974 (m-30) cc_final: 0.8594 (m-30) REVERT: I 75 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: I 156 ASP cc_start: 0.8975 (t0) cc_final: 0.8622 (t0) REVERT: L 8 ASN cc_start: 0.8759 (t0) cc_final: 0.8178 (t0) REVERT: L 140 ARG cc_start: 0.7825 (tmt170) cc_final: 0.7147 (tmt170) outliers start: 23 outliers final: 15 residues processed: 175 average time/residue: 1.6438 time to fit residues: 313.7442 Evaluate side-chains 175 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 205 MET 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 F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 205 MET 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: 0.6980 chunk 102 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 chunk 152 optimal weight: 0.5980 chunk 160 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076198 restraints weight = 40336.796| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.63 r_work: 0.2971 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 16728 Z= 0.119 Angle : 0.578 8.263 22864 Z= 0.271 Chirality : 0.042 0.150 2552 Planarity : 0.005 0.069 2806 Dihedral : 9.959 81.468 2684 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.91 % Allowed : 12.05 % 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: 1.89 (0.20), residues: 1940 helix: 2.89 (0.17), residues: 978 sheet: 0.25 (0.34), residues: 220 loop : -0.74 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 PHE 0.010 0.001 PHE A 131 TYR 0.007 0.001 TYR J 80 ARG 0.009 0.000 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.05607 ( 805) hydrogen bonds : angle 3.54385 ( 2285) metal coordination : bond 0.00383 ( 8) metal coordination : angle 5.54352 ( 6) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.56852 ( 4) covalent geometry : bond 0.00267 (16704) covalent geometry : angle 0.57155 (22854) Misc. bond : bond 0.07024 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20104.52 seconds wall clock time: 346 minutes 10.48 seconds (20770.48 seconds total)