Starting phenix.real_space_refine on Tue Jun 25 19:53:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trk_26099/06_2024/7trk_26099_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trk_26099/06_2024/7trk_26099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trk_26099/06_2024/7trk_26099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trk_26099/06_2024/7trk_26099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trk_26099/06_2024/7trk_26099_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trk_26099/06_2024/7trk_26099_updated.pdb" } resolution = 2.8 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5523 2.51 5 N 1457 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8659 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2106 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 418 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1778 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1764 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: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'IXO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.68, per 1000 atoms: 0.77 Number of scatterers: 8659 At special positions: 0 Unit cell: (92.96, 118.69, 122.84, 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 63 16.00 O 1616 8.00 N 1457 7.00 C 5523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 34.9% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'R' and resid 33 through 59 Processing helix chain 'R' and resid 66 through 95 removed outlier: 4.148A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 135 removed outlier: 3.905A pdb=" N ASP R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU R 107 " --> pdb=" O VAL R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 146 through 175 Proline residue: R 166 - end of helix removed outlier: 5.203A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 220 Processing helix chain 'R' and resid 393 through 423 removed outlier: 3.814A pdb=" N PHE R 409 " --> pdb=" O ILE R 405 " (cutoff:3.500A) Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 432 through 453 removed outlier: 4.280A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 458 through 465 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 31 through 36 removed outlier: 6.050A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.694A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 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 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.903A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (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: 4.473A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.868A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.876A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.714A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.712A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.639A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.527A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.604A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.730A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.580A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.662A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 319 through 322 removed outlier: 6.568A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1161 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: 2.33 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1402 1.32 - 1.44: 2469 1.44 - 1.57: 4880 1.57 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 8843 Sorted by residual: bond pdb=" C10 IXO R 501 " pdb=" N11 IXO R 501 " ideal model delta sigma weight residual 1.270 1.469 -0.199 2.00e-02 2.50e+03 9.91e+01 bond pdb=" C10 IXO R 501 " pdb=" C14 IXO R 501 " ideal model delta sigma weight residual 1.492 1.345 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" C13 IXO R 501 " pdb=" O12 IXO R 501 " ideal model delta sigma weight residual 1.439 1.542 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C10 IXO R 501 " pdb=" O09 IXO R 501 " ideal model delta sigma weight residual 1.325 1.406 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C07 IXO R 501 " pdb=" C08 IXO R 501 " ideal model delta sigma weight residual 1.454 1.534 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 8838 not shown) Histogram of bond angle deviations from ideal: 98.51 - 114.81: 5447 114.81 - 131.10: 6528 131.10 - 147.39: 39 147.39 - 163.69: 0 163.69 - 179.98: 2 Bond angle restraints: 12016 Sorted by residual: angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 123.93 129.45 -5.52 1.54e+00 4.22e-01 1.28e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C TYR R 92 " pdb=" N ILE R 93 " pdb=" CA ILE R 93 " ideal model delta sigma weight residual 121.35 115.87 5.48 1.58e+00 4.01e-01 1.20e+01 angle pdb=" C ASP H 201 " pdb=" N ARG H 202 " pdb=" CA ARG H 202 " ideal model delta sigma weight residual 120.38 125.08 -4.70 1.46e+00 4.69e-01 1.04e+01 angle pdb=" N SER R 191 " pdb=" CA SER R 191 " pdb=" C SER R 191 " ideal model delta sigma weight residual 112.45 108.07 4.38 1.39e+00 5.18e-01 9.95e+00 ... (remaining 12011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 4999 21.04 - 42.08: 182 42.08 - 63.12: 25 63.12 - 84.16: 5 84.16 - 105.21: 1 Dihedral angle restraints: 5212 sinusoidal: 1940 harmonic: 3272 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN B 259 " pdb=" C GLN B 259 " pdb=" N GLU B 260 " pdb=" CA GLU B 260 " ideal model delta harmonic sigma weight residual 180.00 161.34 18.66 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" C05 IXO R 501 " pdb=" C06 IXO R 501 " pdb=" C07 IXO R 501 " pdb=" C08 IXO R 501 " ideal model delta sinusoidal sigma weight residual -178.63 -73.42 -105.21 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 5209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1091 0.065 - 0.131: 245 0.131 - 0.196: 44 0.196 - 0.261: 5 0.261 - 0.327: 3 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB VAL B 71 " pdb=" CA VAL B 71 " pdb=" CG1 VAL B 71 " pdb=" CG2 VAL B 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE R 94 " pdb=" CA ILE R 94 " pdb=" CG1 ILE R 94 " pdb=" CG2 ILE R 94 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PHE R 189 " pdb=" N PHE R 189 " pdb=" C PHE R 189 " pdb=" CB PHE R 189 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1385 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 196 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C THR R 196 " -0.047 2.00e-02 2.50e+03 pdb=" O THR R 196 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE R 197 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 236 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 189 " 0.025 2.00e-02 2.50e+03 1.93e-02 6.54e+00 pdb=" CG PHE R 189 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 189 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 189 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 189 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 189 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 189 " 0.006 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1847 2.78 - 3.31: 7738 3.31 - 3.84: 14723 3.84 - 4.37: 17882 4.37 - 4.90: 30671 Nonbonded interactions: 72861 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.253 2.440 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 443 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.289 2.440 nonbonded pdb=" O GLU R 395 " pdb=" OG1 THR R 399 " model vdw 2.303 2.440 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.306 2.440 ... (remaining 72856 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: 2.590 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: 0.030 Extract box with map and model: 4.010 Check model and map are aligned: 0.160 Set scattering table: 0.270 Process input model: 28.420 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.006 0.199 8843 Z= 0.372 Angle : 0.888 8.674 12016 Z= 0.511 Chirality : 0.058 0.327 1388 Planarity : 0.007 0.067 1511 Dihedral : 11.327 105.205 3088 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.11 % Allowed : 1.52 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.00 (0.23), residues: 1110 helix: -0.71 (0.24), residues: 395 sheet: 0.33 (0.30), residues: 278 loop : -1.13 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.044 0.003 PHE R 189 TYR 0.019 0.002 TYR R 416 ARG 0.004 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8344 (mt0) cc_final: 0.7735 (mt0) REVERT: R 107 LEU cc_start: 0.8106 (mt) cc_final: 0.7737 (tm) REVERT: R 143 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7517 (mtm110) REVERT: R 223 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.8089 (ptm160) REVERT: R 465 ARG cc_start: 0.7863 (ttt90) cc_final: 0.6987 (tpt170) REVERT: B 10 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8477 (tp30) REVERT: B 61 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8609 (ppp) REVERT: B 254 ASP cc_start: 0.8202 (t70) cc_final: 0.7950 (t0) REVERT: G 20 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8602 (mtmp) REVERT: G 24 ASN cc_start: 0.9040 (m-40) cc_final: 0.8769 (m-40) REVERT: H 148 PRO cc_start: 0.9326 (Cg_exo) cc_final: 0.9053 (Cg_endo) REVERT: H 192 MET cc_start: 0.8923 (ttp) cc_final: 0.8720 (ttm) REVERT: H 223 ASP cc_start: 0.8921 (m-30) cc_final: 0.8696 (m-30) REVERT: H 234 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7731 (mt-10) REVERT: H 244 LYS cc_start: 0.9176 (tttt) cc_final: 0.8835 (ttmm) REVERT: A 9 ASP cc_start: 0.8497 (m-30) cc_final: 0.8085 (m-30) REVERT: A 24 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7738 (ttm110) REVERT: A 188 HIS cc_start: 0.8046 (m-70) cc_final: 0.7654 (m-70) REVERT: A 329 THR cc_start: 0.8189 (m) cc_final: 0.7962 (t) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 1.4805 time to fit residues: 307.8298 Evaluate side-chains 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 60 ASN R 117 ASN R 172 GLN R 192 ASN B 13 GLN B 75 GLN B 340 ASN G 18 GLN H 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8843 Z= 0.246 Angle : 0.536 7.348 12016 Z= 0.290 Chirality : 0.042 0.135 1388 Planarity : 0.004 0.050 1511 Dihedral : 4.727 26.627 1223 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.38 % Allowed : 9.20 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.17 (0.24), residues: 1110 helix: 0.80 (0.26), residues: 398 sheet: 0.45 (0.30), residues: 278 loop : -0.67 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.001 PHE R 189 TYR 0.014 0.001 TYR R 89 ARG 0.004 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 54 MET cc_start: 0.7876 (mtm) cc_final: 0.7603 (mtp) REVERT: R 64 GLN cc_start: 0.8295 (mt0) cc_final: 0.7680 (mt0) REVERT: R 97 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6820 (p90) REVERT: R 107 LEU cc_start: 0.8148 (mt) cc_final: 0.7853 (tm) REVERT: R 143 ARG cc_start: 0.7625 (ptm160) cc_final: 0.7295 (mtm110) REVERT: R 223 ARG cc_start: 0.8411 (ptp-170) cc_final: 0.8131 (ptm160) REVERT: R 465 ARG cc_start: 0.7831 (ttt90) cc_final: 0.6930 (tpt170) REVERT: B 13 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: B 61 MET cc_start: 0.8990 (ppp) cc_final: 0.8603 (ppp) REVERT: B 215 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8220 (mp0) REVERT: B 217 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7336 (pmt) REVERT: B 254 ASP cc_start: 0.8150 (t70) cc_final: 0.7899 (t0) REVERT: G 20 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8511 (mtmp) REVERT: G 24 ASN cc_start: 0.8989 (m-40) cc_final: 0.8710 (m-40) REVERT: H 234 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 9 ASP cc_start: 0.8508 (m-30) cc_final: 0.8118 (m-30) REVERT: A 242 ARG cc_start: 0.8906 (mmm-85) cc_final: 0.8558 (mmm-85) REVERT: A 261 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8900 (p0) outliers start: 22 outliers final: 9 residues processed: 159 average time/residue: 1.4444 time to fit residues: 241.7834 Evaluate side-chains 148 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN G 18 GLN H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8843 Z= 0.327 Angle : 0.547 6.993 12016 Z= 0.294 Chirality : 0.043 0.143 1388 Planarity : 0.004 0.043 1511 Dihedral : 4.509 24.458 1220 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.49 % Allowed : 11.36 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.58 (0.25), residues: 1110 helix: 1.37 (0.27), residues: 398 sheet: 0.40 (0.29), residues: 282 loop : -0.48 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE R 189 TYR 0.017 0.001 TYR H 190 ARG 0.003 0.000 ARG R 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8323 (mt0) cc_final: 0.7693 (mt0) REVERT: R 86 MET cc_start: 0.6992 (ttm) cc_final: 0.6783 (ttm) REVERT: R 97 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.6867 (p90) REVERT: R 107 LEU cc_start: 0.8173 (mt) cc_final: 0.7893 (tm) REVERT: R 143 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7278 (mtm110) REVERT: R 223 ARG cc_start: 0.8345 (ptp-170) cc_final: 0.7961 (ptp-170) REVERT: R 407 LEU cc_start: 0.7921 (tp) cc_final: 0.7677 (mm) REVERT: R 465 ARG cc_start: 0.7814 (ttt90) cc_final: 0.6918 (tpt170) REVERT: B 10 GLU cc_start: 0.8723 (tp30) cc_final: 0.8089 (tp30) REVERT: B 130 GLU cc_start: 0.8733 (mp0) cc_final: 0.8356 (mp0) REVERT: B 215 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8189 (mp0) REVERT: B 217 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7315 (pmt) REVERT: B 254 ASP cc_start: 0.8126 (t70) cc_final: 0.7898 (t0) REVERT: G 20 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8399 (mtmp) REVERT: G 24 ASN cc_start: 0.8987 (m-40) cc_final: 0.8707 (m-40) REVERT: H 140 MET cc_start: 0.9332 (mmm) cc_final: 0.8852 (mmm) REVERT: H 234 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7662 (mt-10) REVERT: A 261 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8916 (p0) outliers start: 23 outliers final: 9 residues processed: 159 average time/residue: 1.4933 time to fit residues: 249.6834 Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN B 75 GLN B 259 GLN G 18 GLN H 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8843 Z= 0.161 Angle : 0.522 11.270 12016 Z= 0.273 Chirality : 0.041 0.157 1388 Planarity : 0.003 0.040 1511 Dihedral : 4.447 27.189 1220 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.95 % Allowed : 12.23 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.74 (0.25), residues: 1110 helix: 1.58 (0.27), residues: 398 sheet: 0.36 (0.29), residues: 281 loop : -0.37 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS H 35 PHE 0.016 0.001 PHE R 189 TYR 0.017 0.001 TYR A 296 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8313 (mt0) cc_final: 0.7662 (mt0) REVERT: R 97 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6880 (p90) REVERT: R 107 LEU cc_start: 0.8145 (mt) cc_final: 0.7897 (tm) REVERT: R 143 ARG cc_start: 0.7577 (ptm160) cc_final: 0.7308 (mtm110) REVERT: R 152 MET cc_start: 0.8042 (mtm) cc_final: 0.7823 (mtp) REVERT: R 395 GLU cc_start: 0.7115 (tt0) cc_final: 0.6557 (tt0) REVERT: R 407 LEU cc_start: 0.7918 (tp) cc_final: 0.7696 (mm) REVERT: R 439 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: R 465 ARG cc_start: 0.7820 (ttt90) cc_final: 0.6904 (tpt170) REVERT: B 10 GLU cc_start: 0.8810 (tp30) cc_final: 0.8390 (tp30) REVERT: B 13 GLN cc_start: 0.8471 (pp30) cc_final: 0.8068 (pp30) REVERT: B 130 GLU cc_start: 0.8695 (mp0) cc_final: 0.8283 (mp0) REVERT: B 215 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8193 (mp0) REVERT: B 217 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7548 (pmt) REVERT: B 254 ASP cc_start: 0.8113 (t70) cc_final: 0.7888 (t0) REVERT: G 20 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8156 (mtmt) REVERT: G 24 ASN cc_start: 0.8964 (m-40) cc_final: 0.8668 (m-40) REVERT: G 58 GLU cc_start: 0.8447 (pm20) cc_final: 0.8220 (pm20) REVERT: H 140 MET cc_start: 0.9275 (mmm) cc_final: 0.8818 (mmm) REVERT: H 234 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 261 ASP cc_start: 0.9154 (OUTLIER) cc_final: 0.8894 (p0) outliers start: 18 outliers final: 11 residues processed: 151 average time/residue: 1.5525 time to fit residues: 246.2206 Evaluate side-chains 151 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 0.0010 chunk 26 optimal weight: 3.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8843 Z= 0.261 Angle : 0.532 10.074 12016 Z= 0.280 Chirality : 0.042 0.134 1388 Planarity : 0.004 0.064 1511 Dihedral : 4.387 26.193 1220 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.49 % Allowed : 12.88 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.25), residues: 1110 helix: 1.63 (0.27), residues: 399 sheet: 0.37 (0.29), residues: 283 loop : -0.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.017 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8306 (mt0) cc_final: 0.7646 (mt0) REVERT: R 97 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6867 (p90) REVERT: R 107 LEU cc_start: 0.8144 (mt) cc_final: 0.7896 (tm) REVERT: R 143 ARG cc_start: 0.7582 (ptm160) cc_final: 0.7306 (mtm110) REVERT: R 407 LEU cc_start: 0.7899 (tp) cc_final: 0.7672 (mm) REVERT: R 439 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: R 465 ARG cc_start: 0.7818 (ttt90) cc_final: 0.6917 (tpt170) REVERT: B 10 GLU cc_start: 0.8717 (tp30) cc_final: 0.8456 (tp30) REVERT: B 13 GLN cc_start: 0.8477 (pp30) cc_final: 0.8117 (pp30) REVERT: B 215 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8460 (mp0) REVERT: B 254 ASP cc_start: 0.8120 (t70) cc_final: 0.7915 (t0) REVERT: G 20 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8432 (mtmp) REVERT: G 24 ASN cc_start: 0.8971 (m-40) cc_final: 0.8667 (m-40) REVERT: H 234 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 261 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8900 (p0) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 1.4760 time to fit residues: 240.6982 Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8843 Z= 0.261 Angle : 0.532 10.074 12016 Z= 0.280 Chirality : 0.042 0.134 1388 Planarity : 0.004 0.064 1511 Dihedral : 4.387 26.179 1220 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.62 % Allowed : 14.72 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.25), residues: 1110 helix: 1.63 (0.27), residues: 399 sheet: 0.37 (0.29), residues: 283 loop : -0.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.017 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8306 (mt0) cc_final: 0.7646 (mt0) REVERT: R 97 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6867 (p90) REVERT: R 107 LEU cc_start: 0.8144 (mt) cc_final: 0.7896 (tm) REVERT: R 143 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7306 (mtm110) REVERT: R 407 LEU cc_start: 0.7920 (tp) cc_final: 0.7672 (mm) REVERT: R 439 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: R 465 ARG cc_start: 0.7818 (ttt90) cc_final: 0.6917 (tpt170) REVERT: B 10 GLU cc_start: 0.8719 (tp30) cc_final: 0.8456 (tp30) REVERT: B 13 GLN cc_start: 0.8407 (pp30) cc_final: 0.8117 (pp30) REVERT: B 254 ASP cc_start: 0.8120 (t70) cc_final: 0.7915 (t0) REVERT: G 20 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8432 (mtmp) REVERT: G 24 ASN cc_start: 0.8971 (m-40) cc_final: 0.8667 (m-40) REVERT: H 234 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 261 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8900 (p0) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 1.5319 time to fit residues: 233.3585 Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8843 Z= 0.261 Angle : 0.532 10.074 12016 Z= 0.280 Chirality : 0.042 0.134 1388 Planarity : 0.004 0.064 1511 Dihedral : 4.387 26.179 1220 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.62 % Allowed : 14.72 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.25), residues: 1110 helix: 1.63 (0.27), residues: 399 sheet: 0.37 (0.29), residues: 283 loop : -0.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.017 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8306 (mt0) cc_final: 0.7646 (mt0) REVERT: R 97 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6867 (p90) REVERT: R 107 LEU cc_start: 0.8144 (mt) cc_final: 0.7896 (tm) REVERT: R 143 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7306 (mtm110) REVERT: R 407 LEU cc_start: 0.7920 (tp) cc_final: 0.7672 (mm) REVERT: R 439 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: R 465 ARG cc_start: 0.7818 (ttt90) cc_final: 0.6917 (tpt170) REVERT: B 10 GLU cc_start: 0.8719 (tp30) cc_final: 0.8456 (tp30) REVERT: B 13 GLN cc_start: 0.8408 (pp30) cc_final: 0.8117 (pp30) REVERT: B 254 ASP cc_start: 0.8120 (t70) cc_final: 0.7915 (t0) REVERT: G 20 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8432 (mtmp) REVERT: G 24 ASN cc_start: 0.8971 (m-40) cc_final: 0.8667 (m-40) REVERT: H 234 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 261 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8900 (p0) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 1.5278 time to fit residues: 232.7861 Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8843 Z= 0.261 Angle : 0.532 10.074 12016 Z= 0.280 Chirality : 0.042 0.134 1388 Planarity : 0.004 0.064 1511 Dihedral : 4.387 26.179 1220 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.62 % Allowed : 14.72 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.25), residues: 1110 helix: 1.63 (0.27), residues: 399 sheet: 0.37 (0.29), residues: 283 loop : -0.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.017 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.017 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8306 (mt0) cc_final: 0.7646 (mt0) REVERT: R 97 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6867 (p90) REVERT: R 107 LEU cc_start: 0.8144 (mt) cc_final: 0.7896 (tm) REVERT: R 143 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7306 (mtm110) REVERT: R 407 LEU cc_start: 0.7920 (tp) cc_final: 0.7672 (mm) REVERT: R 439 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: R 465 ARG cc_start: 0.7818 (ttt90) cc_final: 0.6917 (tpt170) REVERT: B 10 GLU cc_start: 0.8719 (tp30) cc_final: 0.8456 (tp30) REVERT: B 13 GLN cc_start: 0.8408 (pp30) cc_final: 0.8117 (pp30) REVERT: B 254 ASP cc_start: 0.8120 (t70) cc_final: 0.7915 (t0) REVERT: G 20 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8432 (mtmp) REVERT: G 24 ASN cc_start: 0.8971 (m-40) cc_final: 0.8667 (m-40) REVERT: H 234 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 261 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8900 (p0) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 1.5238 time to fit residues: 232.2663 Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8843 Z= 0.240 Angle : 0.559 14.095 12016 Z= 0.291 Chirality : 0.042 0.168 1388 Planarity : 0.003 0.042 1511 Dihedral : 4.389 28.713 1220 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.06 % Allowed : 14.39 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.85 (0.25), residues: 1110 helix: 1.69 (0.27), residues: 399 sheet: 0.42 (0.29), residues: 284 loop : -0.33 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 440 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.001 PHE R 189 TYR 0.024 0.001 TYR A 296 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8237 (mt0) cc_final: 0.7598 (mt0) REVERT: R 97 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6869 (p90) REVERT: R 107 LEU cc_start: 0.8163 (mt) cc_final: 0.7927 (tm) REVERT: R 143 ARG cc_start: 0.7577 (ptm160) cc_final: 0.7299 (mtm110) REVERT: R 148 MET cc_start: 0.7281 (tpp) cc_final: 0.7005 (tpp) REVERT: R 407 LEU cc_start: 0.7953 (tp) cc_final: 0.7729 (mm) REVERT: R 439 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: R 465 ARG cc_start: 0.7814 (ttt90) cc_final: 0.6904 (tpt170) REVERT: B 10 GLU cc_start: 0.8733 (tp30) cc_final: 0.8444 (tp30) REVERT: B 13 GLN cc_start: 0.8448 (pp30) cc_final: 0.8131 (pp30) REVERT: B 215 GLU cc_start: 0.8105 (mp0) cc_final: 0.7871 (mp0) REVERT: G 20 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8457 (mtmp) REVERT: G 24 ASN cc_start: 0.8984 (m-40) cc_final: 0.8667 (m-40) REVERT: H 140 MET cc_start: 0.9314 (mmm) cc_final: 0.8882 (mmm) REVERT: H 234 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 240 MET cc_start: 0.8272 (tpt) cc_final: 0.7824 (tpt) REVERT: A 261 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8898 (p0) outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 1.5294 time to fit residues: 249.6623 Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 18 GLN H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8843 Z= 0.240 Angle : 0.559 14.095 12016 Z= 0.291 Chirality : 0.042 0.168 1388 Planarity : 0.003 0.042 1511 Dihedral : 4.389 28.713 1220 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 15.48 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.85 (0.25), residues: 1110 helix: 1.69 (0.27), residues: 399 sheet: 0.42 (0.29), residues: 284 loop : -0.33 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 440 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.001 PHE R 189 TYR 0.024 0.001 TYR A 296 ARG 0.008 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: R 64 GLN cc_start: 0.8237 (mt0) cc_final: 0.7598 (mt0) REVERT: R 97 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6868 (p90) REVERT: R 107 LEU cc_start: 0.8163 (mt) cc_final: 0.7927 (tm) REVERT: R 143 ARG cc_start: 0.7577 (ptm160) cc_final: 0.7299 (mtm110) REVERT: R 148 MET cc_start: 0.7268 (tpp) cc_final: 0.7005 (tpp) REVERT: R 407 LEU cc_start: 0.7958 (tp) cc_final: 0.7729 (mm) REVERT: R 439 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6830 (m-80) REVERT: R 465 ARG cc_start: 0.7814 (ttt90) cc_final: 0.6904 (tpt170) REVERT: B 10 GLU cc_start: 0.8735 (tp30) cc_final: 0.8444 (tp30) REVERT: B 13 GLN cc_start: 0.8448 (pp30) cc_final: 0.8131 (pp30) REVERT: B 215 GLU cc_start: 0.8103 (mp0) cc_final: 0.7871 (mp0) REVERT: G 20 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8457 (mtmp) REVERT: G 24 ASN cc_start: 0.8984 (m-40) cc_final: 0.8667 (m-40) REVERT: H 140 MET cc_start: 0.9314 (mmm) cc_final: 0.8882 (mmm) REVERT: H 234 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 240 MET cc_start: 0.8272 (tpt) cc_final: 0.7824 (tpt) REVERT: A 261 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8898 (p0) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 1.4640 time to fit residues: 232.7670 Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 TYR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain R residue 439 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 18 GLN H 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.061980 restraints weight = 16640.893| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.83 r_work: 0.2639 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8843 Z= 0.240 Angle : 0.559 14.095 12016 Z= 0.291 Chirality : 0.042 0.168 1388 Planarity : 0.003 0.042 1511 Dihedral : 4.389 28.713 1220 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 15.58 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.85 (0.25), residues: 1110 helix: 1.69 (0.27), residues: 399 sheet: 0.42 (0.29), residues: 284 loop : -0.33 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 440 HIS 0.003 0.001 HIS H 35 PHE 0.017 0.001 PHE R 189 TYR 0.024 0.001 TYR A 296 ARG 0.008 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4177.84 seconds wall clock time: 73 minutes 14.76 seconds (4394.76 seconds total)