Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:12:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/04_2023/8id4_35357_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/04_2023/8id4_35357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/04_2023/8id4_35357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/04_2023/8id4_35357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/04_2023/8id4_35357_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/04_2023/8id4_35357_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.016 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2174 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1761 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2572 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 404 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1733 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'EIC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8665 At special positions: 0 Unit cell: (106.47, 127.764, 113.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.5% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 39 through 68 removed outlier: 3.619A pdb=" N ARG R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 100 removed outlier: 3.526A pdb=" N PHE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 114 through 141 Processing helix chain 'R' and resid 152 through 173 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 202 through 215 removed outlier: 3.662A pdb=" N SER R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR R 213 " --> pdb=" O VAL R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 243 removed outlier: 3.663A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 293 removed outlier: 3.864A pdb=" N SER R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) Proline residue: R 279 - end of helix removed outlier: 3.849A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 320 removed outlier: 3.537A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.921A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 removed outlier: 4.619A pdb=" N GLU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU A 276 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.938A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.744A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.636A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 43 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'R' and resid 177 through 181 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.556A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.850A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.754A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.502A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.587A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.745A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.453A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.594A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.692A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 95 through 99 removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 147 through 149 removed outlier: 6.802A pdb=" N LYS S 245 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 156 through 161 removed outlier: 3.522A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2378 1.33 - 1.45: 1616 1.45 - 1.57: 4759 1.57 - 1.70: 2 1.70 - 1.82: 83 Bond restraints: 8838 Sorted by residual: bond pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.12e+01 bond pdb=" CA PHE R 88 " pdb=" C PHE R 88 " ideal model delta sigma weight residual 1.524 1.584 -0.061 1.27e-02 6.20e+03 2.28e+01 bond pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.20e-02 6.94e+03 1.55e+01 bond pdb=" N ILE R 89 " pdb=" CA ILE R 89 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.23e-02 6.61e+03 8.84e+00 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.31: 128 105.31 - 112.49: 4604 112.49 - 119.67: 2821 119.67 - 126.85: 4326 126.85 - 134.03: 113 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ALA A 326 " pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 108.38 120.67 -12.29 1.35e+00 5.49e-01 8.29e+01 angle pdb=" N SER R 244 " pdb=" CA SER R 244 " pdb=" C SER R 244 " ideal model delta sigma weight residual 110.28 100.09 10.19 1.48e+00 4.57e-01 4.74e+01 angle pdb=" N ARG R 69 " pdb=" CA ARG R 69 " pdb=" C ARG R 69 " ideal model delta sigma weight residual 112.90 106.20 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" N SER R 90 " pdb=" CA SER R 90 " pdb=" C SER R 90 " ideal model delta sigma weight residual 112.34 105.71 6.63 1.30e+00 5.92e-01 2.60e+01 angle pdb=" N ILE R 89 " pdb=" CA ILE R 89 " pdb=" C ILE R 89 " ideal model delta sigma weight residual 111.44 117.93 -6.49 1.34e+00 5.57e-01 2.34e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4753 16.82 - 33.64: 377 33.64 - 50.46: 68 50.46 - 67.29: 10 67.29 - 84.11: 9 Dihedral angle restraints: 5217 sinusoidal: 1934 harmonic: 3283 Sorted by residual: dihedral pdb=" C THR A 327 " pdb=" N THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual -122.00 -145.78 23.78 0 2.50e+00 1.60e-01 9.05e+01 dihedral pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual 123.40 145.69 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" CA ILE R 298 " pdb=" C ILE R 298 " pdb=" N TRP R 299 " pdb=" CA TRP R 299 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 1391 0.171 - 0.342: 8 0.342 - 0.514: 0 0.514 - 0.685: 0 0.685 - 0.856: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 1.67 0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" CB ILE R 197 " pdb=" CA ILE R 197 " pdb=" CG1 ILE R 197 " pdb=" CG2 ILE R 197 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER R 244 " pdb=" N SER R 244 " pdb=" C SER R 244 " pdb=" CB SER R 244 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1397 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO R 172 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 324 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.70e+00 pdb=" C THR A 324 " -0.054 2.00e-02 2.50e+03 pdb=" O THR A 324 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.050 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO S 14 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.041 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1204 2.75 - 3.29: 8085 3.29 - 3.83: 13946 3.83 - 4.36: 16927 4.36 - 4.90: 30351 Nonbonded interactions: 70513 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.217 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.233 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 176 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 2.440 ... (remaining 70508 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.370 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: 0.000 Extract box with map and model: 2.300 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.370 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.004 0.095 8838 Z= 0.284 Angle : 0.732 12.295 11992 Z= 0.427 Chirality : 0.053 0.856 1400 Planarity : 0.005 0.078 1508 Dihedral : 12.922 84.108 3088 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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: -1.06 (0.25), residues: 1112 helix: 0.33 (0.28), residues: 370 sheet: -0.43 (0.31), residues: 276 loop : -1.68 (0.27), residues: 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.994 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2644 time to fit residues: 46.5268 Evaluate side-chains 117 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.0050 chunk 28 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 215 ASN A 306 GLN B 17 GLN B 91 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8838 Z= 0.134 Angle : 0.502 7.658 11992 Z= 0.266 Chirality : 0.041 0.230 1400 Planarity : 0.004 0.060 1508 Dihedral : 5.288 70.526 1227 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.62 (0.25), residues: 1112 helix: 0.84 (0.28), residues: 375 sheet: -0.22 (0.29), residues: 279 loop : -1.55 (0.27), residues: 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.073 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 127 average time/residue: 0.2575 time to fit residues: 43.6656 Evaluate side-chains 119 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0851 time to fit residues: 2.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 27 optimal weight: 0.1980 chunk 100 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 8838 Z= 0.141 Angle : 0.484 7.821 11992 Z= 0.256 Chirality : 0.041 0.222 1400 Planarity : 0.004 0.053 1508 Dihedral : 5.023 70.673 1227 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1112 helix: 1.06 (0.28), residues: 376 sheet: -0.03 (0.29), residues: 279 loop : -1.44 (0.27), residues: 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.003 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 127 average time/residue: 0.2515 time to fit residues: 43.1208 Evaluate side-chains 112 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0860 time to fit residues: 1.9648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.0170 chunk 28 optimal weight: 0.0030 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.3306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 8838 Z= 0.114 Angle : 0.454 6.844 11992 Z= 0.241 Chirality : 0.040 0.180 1400 Planarity : 0.003 0.050 1508 Dihedral : 4.788 71.072 1227 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.61 % Favored : 97.21 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.07 (0.25), residues: 1112 helix: 1.37 (0.28), residues: 376 sheet: 0.09 (0.29), residues: 291 loop : -1.37 (0.27), residues: 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.072 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 127 average time/residue: 0.2356 time to fit residues: 40.8040 Evaluate side-chains 113 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0868 time to fit residues: 2.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 8838 Z= 0.441 Angle : 0.632 8.995 11992 Z= 0.334 Chirality : 0.047 0.229 1400 Planarity : 0.005 0.063 1508 Dihedral : 5.472 71.371 1227 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.95 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.36 (0.25), residues: 1112 helix: 1.02 (0.27), residues: 372 sheet: 0.04 (0.29), residues: 291 loop : -1.50 (0.28), residues: 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.911 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.2379 time to fit residues: 37.3940 Evaluate side-chains 112 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0952 time to fit residues: 2.2414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 8838 Z= 0.134 Angle : 0.475 6.463 11992 Z= 0.251 Chirality : 0.041 0.249 1400 Planarity : 0.004 0.049 1508 Dihedral : 4.997 71.654 1227 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1112 helix: 1.35 (0.28), residues: 376 sheet: 0.13 (0.29), residues: 291 loop : -1.30 (0.28), residues: 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.099 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 121 average time/residue: 0.2549 time to fit residues: 41.4408 Evaluate side-chains 117 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0851 time to fit residues: 2.2129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 8838 Z= 0.408 Angle : 0.622 8.463 11992 Z= 0.328 Chirality : 0.046 0.261 1400 Planarity : 0.004 0.062 1508 Dihedral : 5.464 71.508 1227 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.34 (0.25), residues: 1112 helix: 0.97 (0.27), residues: 378 sheet: 0.06 (0.29), residues: 290 loop : -1.44 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.013 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 117 average time/residue: 0.2603 time to fit residues: 40.7060 Evaluate side-chains 112 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0980 time to fit residues: 1.9453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8838 Z= 0.144 Angle : 0.502 8.043 11992 Z= 0.262 Chirality : 0.041 0.274 1400 Planarity : 0.004 0.050 1508 Dihedral : 5.043 71.944 1227 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1112 helix: 1.39 (0.28), residues: 376 sheet: 0.13 (0.30), residues: 285 loop : -1.33 (0.28), residues: 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.131 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.2470 time to fit residues: 38.3268 Evaluate side-chains 112 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0801 time to fit residues: 1.8196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8838 Z= 0.193 Angle : 0.516 6.817 11992 Z= 0.271 Chirality : 0.042 0.263 1400 Planarity : 0.004 0.051 1508 Dihedral : 5.069 72.211 1227 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1112 helix: 1.47 (0.28), residues: 376 sheet: 0.16 (0.29), residues: 289 loop : -1.31 (0.28), residues: 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.938 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2546 time to fit residues: 37.1492 Evaluate side-chains 107 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8838 Z= 0.208 Angle : 0.520 7.376 11992 Z= 0.273 Chirality : 0.042 0.255 1400 Planarity : 0.004 0.052 1508 Dihedral : 5.090 72.588 1227 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.25), residues: 1112 helix: 1.53 (0.28), residues: 376 sheet: 0.14 (0.29), residues: 289 loop : -1.29 (0.28), residues: 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.017 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.2543 time to fit residues: 37.2962 Evaluate side-chains 106 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0790 time to fit residues: 1.4946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.172566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.134171 restraints weight = 9277.215| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.36 r_work: 0.3095 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8838 Z= 0.140 Angle : 0.486 7.346 11992 Z= 0.255 Chirality : 0.041 0.255 1400 Planarity : 0.004 0.049 1508 Dihedral : 4.918 73.174 1227 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.28 (0.25), residues: 1112 helix: 1.74 (0.28), residues: 375 sheet: 0.22 (0.29), residues: 295 loop : -1.21 (0.28), residues: 442 =============================================================================== Job complete usr+sys time: 1883.88 seconds wall clock time: 35 minutes 5.18 seconds (2105.18 seconds total)