Starting phenix.real_space_refine on Sun Apr 7 23:49:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k21_22639/04_2024/7k21_22639_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k21_22639/04_2024/7k21_22639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k21_22639/04_2024/7k21_22639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k21_22639/04_2024/7k21_22639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k21_22639/04_2024/7k21_22639_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k21_22639/04_2024/7k21_22639_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7480 2.51 5 N 1984 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11848 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {' MG': 1, '1T4': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.90, per 1000 atoms: 0.58 Number of scatterers: 11848 At special positions: 0 Unit cell: (100.32, 76.285, 164.065, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 2284 8.00 N 1984 7.00 C 7480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.3 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 17 sheets defined 36.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 92 removed outlier: 3.530A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 192 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.684A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.552A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 293 No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 4.230A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 removed outlier: 3.542A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 192 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.693A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.569A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.610A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 317 Processing helix chain 'B' and resid 338 through 347 Processing helix chain 'B' and resid 359 through 369 removed outlier: 4.160A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.540A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 192 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.631A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 229 Processing helix chain 'C' and resid 253 through 256 No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 359 through 369 removed outlier: 4.248A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.514A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 182 through 192 Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.652A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 229 Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 288 through 293 removed outlier: 4.181A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 338 through 347 Processing helix chain 'D' and resid 359 through 369 removed outlier: 4.117A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 8 through 10 removed outlier: 3.838A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 16 through 19 Processing sheet with id= C, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.733A pdb=" N LYS A 68 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.366A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.479A pdb=" N CYS B 10 " --> pdb=" O PRO B 102 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU B 104 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN B 12 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR B 106 " --> pdb=" O ASN B 12 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.565A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.196A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= J, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.935A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 52 through 54 removed outlier: 3.626A pdb=" N LYS C 68 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.213A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= N, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.508A pdb=" N CYS D 10 " --> pdb=" O PRO D 102 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU D 104 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 12 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR D 106 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR D 133 " --> pdb=" O THR D 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 52 through 54 removed outlier: 3.538A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 151 through 154 Processing sheet with id= Q, first strand: chain 'D' and resid 238 through 241 338 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3637 1.33 - 1.45: 1782 1.45 - 1.57: 6533 1.57 - 1.69: 12 1.69 - 1.80: 148 Bond restraints: 12112 Sorted by residual: bond pdb=" O4 PO4 A 803 " pdb=" P PO4 A 803 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 PO4 D 803 " pdb=" P PO4 D 803 " ideal model delta sigma weight residual 1.568 1.501 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O4 PO4 C 803 " pdb=" P PO4 C 803 " ideal model delta sigma weight residual 1.568 1.501 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O3 PO4 B 803 " pdb=" P PO4 B 803 " ideal model delta sigma weight residual 1.569 1.502 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 12107 not shown) Histogram of bond angle deviations from ideal: 98.96 - 106.28: 426 106.28 - 113.60: 6684 113.60 - 120.93: 5686 120.93 - 128.25: 3560 128.25 - 135.57: 96 Bond angle restraints: 16452 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.68 -6.18 1.70e+00 3.46e-01 1.32e+01 angle pdb=" C19 1T4 B 804 " pdb=" C17 1T4 B 804 " pdb=" N1 1T4 B 804 " ideal model delta sigma weight residual 114.67 125.44 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 116.51 -6.01 1.70e+00 3.46e-01 1.25e+01 angle pdb=" C19 1T4 D 804 " pdb=" C17 1T4 D 804 " pdb=" N1 1T4 D 804 " ideal model delta sigma weight residual 114.67 125.18 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C19 1T4 C 804 " pdb=" C17 1T4 C 804 " pdb=" N1 1T4 C 804 " ideal model delta sigma weight residual 114.67 125.01 -10.34 3.00e+00 1.11e-01 1.19e+01 ... (remaining 16447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 6992 20.95 - 41.89: 205 41.89 - 62.84: 9 62.84 - 83.78: 10 83.78 - 104.73: 4 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 -164.73 104.73 1 2.00e+01 2.50e-03 3.01e+01 dihedral pdb=" O1B ADP D 802 " pdb=" O3A ADP D 802 " pdb=" PB ADP D 802 " pdb=" PA ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 -159.76 99.76 1 2.00e+01 2.50e-03 2.81e+01 dihedral pdb=" O1B ADP C 802 " pdb=" O3A ADP C 802 " pdb=" PB ADP C 802 " pdb=" PA ADP C 802 " ideal model delta sinusoidal sigma weight residual -60.00 -157.82 97.82 1 2.00e+01 2.50e-03 2.73e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1288 0.057 - 0.115: 451 0.115 - 0.172: 56 0.172 - 0.229: 5 0.229 - 0.287: 8 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1805 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.50e+00 pdb=" N PRO A 164 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " -0.019 2.00e-02 2.50e+03 1.34e-02 4.48e+00 pdb=" CG TRP D 340 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 340 " -0.019 2.00e-02 2.50e+03 1.31e-02 4.29e+00 pdb=" CG TRP A 340 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 340 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 340 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 340 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 340 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 340 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 340 " -0.003 2.00e-02 2.50e+03 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 161 2.63 - 3.20: 10042 3.20 - 3.77: 18280 3.77 - 4.33: 27633 4.33 - 4.90: 43800 Nonbonded interactions: 99916 Sorted by model distance: nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.066 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.070 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.075 2.170 nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A 202 " pdb=" OE1 GLU A 205 " model vdw 2.223 2.440 ... (remaining 99911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.730 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.100 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.007 0.088 12112 Z= 0.487 Angle : 0.866 10.768 16452 Z= 0.436 Chirality : 0.057 0.287 1808 Planarity : 0.007 0.053 2092 Dihedral : 10.390 104.727 4468 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.23 (0.17), residues: 1468 helix: -4.24 (0.09), residues: 592 sheet: -1.26 (0.41), residues: 136 loop : -1.73 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP D 340 HIS 0.011 0.003 HIS C 88 PHE 0.021 0.003 PHE A 124 TYR 0.030 0.003 TYR C 69 ARG 0.015 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 299 MET cc_start: 0.8549 (mtm) cc_final: 0.8223 (mtm) outliers start: 0 outliers final: 1 residues processed: 125 average time/residue: 1.4666 time to fit residues: 197.6535 Evaluate side-chains 91 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 86 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 87 HIS A 88 HIS A 161 HIS B 40 HIS B 88 HIS B 128 ASN B 161 HIS C 88 HIS C 161 HIS C 296 ASN D 88 HIS D 161 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12112 Z= 0.209 Angle : 0.573 6.363 16452 Z= 0.281 Chirality : 0.045 0.143 1808 Planarity : 0.005 0.050 2092 Dihedral : 8.666 83.149 1674 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.72 % Allowed : 6.85 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.49 (0.19), residues: 1468 helix: -2.47 (0.16), residues: 592 sheet: -1.05 (0.31), residues: 248 loop : -0.79 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 340 HIS 0.004 0.001 HIS C 88 PHE 0.009 0.001 PHE A 90 TYR 0.008 0.001 TYR A 294 ARG 0.004 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.524 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8159 (p0) cc_final: 0.7929 (p0) REVERT: B 299 MET cc_start: 0.8558 (mtm) cc_final: 0.8256 (mtm) outliers start: 9 outliers final: 0 residues processed: 101 average time/residue: 1.3126 time to fit residues: 144.5921 Evaluate side-chains 93 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 296 ASN B 59 GLN C 59 GLN C 353 GLN D 296 ASN D 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 12112 Z= 0.430 Angle : 0.619 6.529 16452 Z= 0.305 Chirality : 0.049 0.155 1808 Planarity : 0.005 0.055 2092 Dihedral : 8.169 84.988 1672 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.04 % Allowed : 8.04 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.05 (0.22), residues: 1468 helix: -1.09 (0.21), residues: 568 sheet: -0.58 (0.32), residues: 244 loop : -0.12 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 340 HIS 0.006 0.002 HIS D 40 PHE 0.014 0.002 PHE D 262 TYR 0.019 0.002 TYR D 69 ARG 0.005 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8418 (p0) cc_final: 0.8202 (p0) REVERT: B 299 MET cc_start: 0.8607 (mtm) cc_final: 0.8377 (mtm) outliers start: 13 outliers final: 2 residues processed: 95 average time/residue: 1.4576 time to fit residues: 150.5058 Evaluate side-chains 86 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12112 Z= 0.180 Angle : 0.524 6.142 16452 Z= 0.249 Chirality : 0.045 0.138 1808 Planarity : 0.004 0.045 2092 Dihedral : 7.746 85.715 1672 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.27 % Allowed : 8.28 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.22), residues: 1468 helix: -0.47 (0.22), residues: 568 sheet: -0.46 (0.32), residues: 248 loop : 0.14 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.003 0.001 HIS A 87 PHE 0.008 0.001 PHE C 31 TYR 0.007 0.001 TYR D 69 ARG 0.003 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: B 299 MET cc_start: 0.8585 (mtm) cc_final: 0.8352 (mtm) outliers start: 16 outliers final: 3 residues processed: 97 average time/residue: 1.2924 time to fit residues: 136.9043 Evaluate side-chains 97 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 25 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 chunk 106 optimal weight: 0.0000 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 0.0050 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12112 Z= 0.128 Angle : 0.508 6.083 16452 Z= 0.239 Chirality : 0.044 0.136 1808 Planarity : 0.003 0.042 2092 Dihedral : 7.501 85.168 1672 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.27 % Allowed : 8.44 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.23), residues: 1468 helix: -0.34 (0.22), residues: 596 sheet: -0.25 (0.32), residues: 248 loop : 0.15 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE C 31 TYR 0.009 0.001 TYR A 69 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: B 299 MET cc_start: 0.8579 (mtm) cc_final: 0.8349 (mtm) outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 1.3696 time to fit residues: 156.1596 Evaluate side-chains 93 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 190 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 28 optimal weight: 0.0060 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 263 GLN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12112 Z= 0.172 Angle : 0.515 6.065 16452 Z= 0.243 Chirality : 0.044 0.135 1808 Planarity : 0.003 0.042 2092 Dihedral : 7.375 84.408 1672 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 9.39 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.23), residues: 1468 helix: -0.17 (0.23), residues: 596 sheet: -0.14 (0.33), residues: 248 loop : 0.25 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE C 31 TYR 0.010 0.001 TYR A 69 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: B 299 MET cc_start: 0.8571 (mtm) cc_final: 0.8347 (mtm) outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 1.3495 time to fit residues: 138.1335 Evaluate side-chains 89 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 25 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12112 Z= 0.211 Angle : 0.524 6.139 16452 Z= 0.248 Chirality : 0.045 0.140 1808 Planarity : 0.003 0.043 2092 Dihedral : 7.377 84.270 1672 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.11 % Allowed : 9.63 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.23), residues: 1468 helix: -0.10 (0.23), residues: 596 sheet: -0.08 (0.33), residues: 248 loop : 0.31 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE C 31 TYR 0.010 0.001 TYR A 69 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 1.452 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8280 (mmt) REVERT: B 299 MET cc_start: 0.8578 (mtm) cc_final: 0.8362 (mtm) outliers start: 14 outliers final: 6 residues processed: 92 average time/residue: 1.3728 time to fit residues: 137.7561 Evaluate side-chains 92 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 25 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 101 HIS B 353 GLN C 49 GLN D 12 ASN D 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12112 Z= 0.387 Angle : 0.589 6.282 16452 Z= 0.285 Chirality : 0.048 0.144 1808 Planarity : 0.004 0.042 2092 Dihedral : 7.760 86.108 1672 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.27 % Allowed : 9.71 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.23), residues: 1468 helix: -0.00 (0.23), residues: 572 sheet: -0.01 (0.35), residues: 204 loop : 0.37 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 340 HIS 0.005 0.001 HIS A 161 PHE 0.011 0.001 PHE D 262 TYR 0.014 0.002 TYR A 306 ARG 0.005 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8407 (mmt) REVERT: A 372 ARG cc_start: 0.8240 (pmm-80) cc_final: 0.7987 (pmm-80) outliers start: 16 outliers final: 8 residues processed: 96 average time/residue: 1.4022 time to fit residues: 146.0741 Evaluate side-chains 95 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 288 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12112 Z= 0.233 Angle : 0.542 6.206 16452 Z= 0.259 Chirality : 0.045 0.141 1808 Planarity : 0.003 0.041 2092 Dihedral : 7.614 86.817 1672 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.04 % Allowed : 10.19 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.23), residues: 1468 helix: -0.13 (0.23), residues: 600 sheet: -0.10 (0.35), residues: 208 loop : 0.36 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS A 161 PHE 0.007 0.001 PHE C 31 TYR 0.010 0.001 TYR A 69 ARG 0.003 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7410 (pm20) cc_final: 0.7188 (pm20) REVERT: A 225 ASN cc_start: 0.8504 (m-40) cc_final: 0.8215 (m-40) REVERT: A 305 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8328 (mmt) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 1.4059 time to fit residues: 146.7532 Evaluate side-chains 97 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain D residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.0010 chunk 71 optimal weight: 0.0570 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 overall best weight: 0.5906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12112 Z= 0.173 Angle : 0.527 6.163 16452 Z= 0.250 Chirality : 0.044 0.141 1808 Planarity : 0.003 0.041 2092 Dihedral : 7.450 86.803 1672 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.56 % Allowed : 10.35 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.23), residues: 1468 helix: 0.04 (0.23), residues: 588 sheet: -0.09 (0.35), residues: 208 loop : 0.47 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.007 0.001 PHE C 31 TYR 0.009 0.001 TYR A 69 ARG 0.003 0.000 ARG A 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7368 (pm20) cc_final: 0.7145 (pm20) REVERT: A 225 ASN cc_start: 0.8448 (m-40) cc_final: 0.8163 (m-40) REVERT: A 305 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8267 (mmt) outliers start: 7 outliers final: 7 residues processed: 95 average time/residue: 1.3812 time to fit residues: 142.7844 Evaluate side-chains 96 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain D residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.0050 chunk 120 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8034 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.077774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.064039 restraints weight = 23308.689| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.31 r_work: 0.2756 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12112 Z= 0.209 Angle : 0.532 6.200 16452 Z= 0.252 Chirality : 0.045 0.139 1808 Planarity : 0.003 0.041 2092 Dihedral : 7.393 86.392 1672 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.64 % Allowed : 10.67 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.23), residues: 1468 helix: 0.07 (0.23), residues: 588 sheet: -0.05 (0.35), residues: 208 loop : 0.51 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.003 0.001 HIS A 161 PHE 0.006 0.001 PHE C 31 TYR 0.010 0.001 TYR A 69 ARG 0.003 0.000 ARG B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3541.51 seconds wall clock time: 64 minutes 53.58 seconds (3893.58 seconds total)