Starting phenix.real_space_refine on Thu Feb 13 05:29:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trp_26100/02_2025/7trp_26100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trp_26100/02_2025/7trp_26100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trp_26100/02_2025/7trp_26100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trp_26100/02_2025/7trp_26100.map" model { file = "/net/cci-nas-00/data/ceres_data/7trp_26100/02_2025/7trp_26100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trp_26100/02_2025/7trp_26100.cif" } resolution = 2.4 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 1 4.86 5 C 5535 2.51 5 N 1461 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8681 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2079 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2591 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1768 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'IUE': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.03, per 1000 atoms: 0.58 Number of scatterers: 8681 At special positions: 0 Unit cell: (93.79, 119.52, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 64 16.00 O 1620 8.00 N 1461 7.00 C 5535 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=2.03 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 38.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.624A pdb=" N ASN R 60 " --> pdb=" O SER R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 66 through 84 removed outlier: 4.384A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 Processing helix chain 'R' and resid 102 through 136 Processing helix chain 'R' and resid 145 through 175 Proline residue: R 166 - end of helix removed outlier: 5.184A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.564A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 223 removed outlier: 3.906A pdb=" N ARG R 223 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 426 Proline residue: R 415 - end of helix removed outlier: 3.537A pdb=" N THR R 424 " --> pdb=" O VAL R 420 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 448 removed outlier: 3.798A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 454 Processing helix chain 'R' and resid 457 through 463 removed outlier: 3.625A pdb=" N LYS R 461 " --> pdb=" O ASN R 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.573A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.653A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.355A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.128A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.556A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.628A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.254A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.792A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.812A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.500A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.700A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.994A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.491A 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: 7.265A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.132A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.016A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.611A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.013A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.013A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.626A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.271A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1275 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: 2.83 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1398 1.31 - 1.44: 2469 1.44 - 1.57: 4903 1.57 - 1.69: 1 1.69 - 1.82: 94 Bond restraints: 8865 Sorted by residual: bond pdb=" C10 IXO R 702 " pdb=" N11 IXO R 702 " ideal model delta sigma weight residual 1.270 1.475 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C10 IXO R 702 " pdb=" C14 IXO R 702 " ideal model delta sigma weight residual 1.492 1.331 0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" C13 IXO R 702 " pdb=" O12 IXO R 702 " ideal model delta sigma weight residual 1.439 1.544 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C05 IXO R 702 " pdb=" C06 IXO R 702 " ideal model delta sigma weight residual 1.450 1.528 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C07 IXO R 702 " pdb=" C08 IXO R 702 " ideal model delta sigma weight residual 1.454 1.530 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 8860 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11627 2.00 - 4.00: 356 4.00 - 6.00: 41 6.00 - 8.00: 14 8.00 - 9.99: 3 Bond angle restraints: 12041 Sorted by residual: angle pdb=" N GLY H 209 " pdb=" CA GLY H 209 " pdb=" C GLY H 209 " ideal model delta sigma weight residual 113.18 121.40 -8.22 2.37e+00 1.78e-01 1.20e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N ALA R 165 " pdb=" CA ALA R 165 " pdb=" C ALA R 165 " ideal model delta sigma weight residual 112.75 117.28 -4.53 1.36e+00 5.41e-01 1.11e+01 angle pdb=" CA TRP R 440 " pdb=" CB TRP R 440 " pdb=" CG TRP R 440 " ideal model delta sigma weight residual 113.60 107.43 6.17 1.90e+00 2.77e-01 1.05e+01 angle pdb=" N CYS R 429 " pdb=" CA CYS R 429 " pdb=" C CYS R 429 " ideal model delta sigma weight residual 111.07 114.38 -3.31 1.07e+00 8.73e-01 9.54e+00 ... (remaining 12036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4906 16.99 - 33.98: 270 33.98 - 50.97: 45 50.97 - 67.96: 9 67.96 - 84.95: 4 Dihedral angle restraints: 5234 sinusoidal: 1974 harmonic: 3260 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N LYS A 197 " pdb=" CA LYS A 197 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1099 0.064 - 0.127: 225 0.127 - 0.191: 53 0.191 - 0.255: 5 0.255 - 0.318: 3 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL R 444 " pdb=" CA VAL R 444 " pdb=" CG1 VAL R 444 " pdb=" CG2 VAL R 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB THR R 90 " pdb=" CA THR R 90 " pdb=" OG1 THR R 90 " pdb=" CG2 THR R 90 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1382 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N IUE R 701 " 0.035 2.00e-02 2.50e+03 3.45e-02 4.17e+01 pdb=" C IUE R 701 " -0.023 2.00e-02 2.50e+03 pdb=" O IUE R 701 " -0.039 2.00e-02 2.50e+03 pdb=" C1 IUE R 701 " 0.013 2.00e-02 2.50e+03 pdb=" C2 IUE R 701 " 0.029 2.00e-02 2.50e+03 pdb=" C3 IUE R 701 " 0.014 2.00e-02 2.50e+03 pdb=" C4 IUE R 701 " -0.012 2.00e-02 2.50e+03 pdb=" C5 IUE R 701 " 0.036 2.00e-02 2.50e+03 pdb=" C6 IUE R 701 " 0.004 2.00e-02 2.50e+03 pdb=" C7 IUE R 701 " -0.003 2.00e-02 2.50e+03 pdb=" C9 IUE R 701 " -0.086 2.00e-02 2.50e+03 pdb=" N2 IUE R 701 " 0.046 2.00e-02 2.50e+03 pdb=" S IUE R 701 " 0.016 2.00e-02 2.50e+03 pdb="CL IUE R 701 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IUE R 701 " -0.057 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C4 IUE R 701 " -0.045 2.00e-02 2.50e+03 pdb=" C9 IUE R 701 " 0.021 2.00e-02 2.50e+03 pdb=" N1 IUE R 701 " 0.076 2.00e-02 2.50e+03 pdb=" O1 IUE R 701 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 113 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C TYR R 113 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR R 113 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL R 114 " -0.022 2.00e-02 2.50e+03 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2315 2.81 - 3.33: 7729 3.33 - 3.85: 14628 3.85 - 4.38: 17643 4.38 - 4.90: 30339 Nonbonded interactions: 72654 Sorted by model distance: nonbonded pdb=" OH TYR R 113 " pdb=" OH TYR R 416 " model vdw 2.287 3.040 nonbonded pdb=" O THR R 433 " pdb=" OG SER R 436 " model vdw 2.311 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.324 3.040 nonbonded pdb=" O ASN R 87 " pdb=" OG1 THR R 90 " model vdw 2.329 3.040 ... (remaining 72649 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.950 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.410 Find NCS groups from input model: 0.100 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:13.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 0.205 8865 Z= 0.371 Angle : 0.818 9.994 12041 Z= 0.464 Chirality : 0.056 0.318 1385 Planarity : 0.007 0.085 1511 Dihedral : 11.233 84.947 3118 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.21 % Allowed : 0.64 % Favored : 99.14 % 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: -0.43 (0.23), residues: 1106 helix: -0.02 (0.24), residues: 382 sheet: 0.22 (0.29), residues: 300 loop : -0.74 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 440 HIS 0.004 0.001 HIS H 35 PHE 0.035 0.003 PHE R 189 TYR 0.029 0.002 TYR R 215 ARG 0.006 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 210 ILE cc_start: 0.8052 (mm) cc_final: 0.7814 (mp) REVERT: R 223 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7722 (ttm110) REVERT: B 270 ILE cc_start: 0.9015 (pt) cc_final: 0.8768 (tp) REVERT: H 186 GLN cc_start: 0.8733 (tt0) cc_final: 0.8461 (tt0) REVERT: H 220 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7958 (mm-30) REVERT: A 302 TYR cc_start: 0.8938 (t80) cc_final: 0.8697 (t80) REVERT: A 306 GLN cc_start: 0.8868 (mm110) cc_final: 0.8296 (mp10) REVERT: A 308 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8352 (mt-10) outliers start: 2 outliers final: 0 residues processed: 163 average time/residue: 1.6869 time to fit residues: 288.3797 Evaluate side-chains 123 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 ASN R 117 ASN R 172 GLN B 268 ASN H 39 GLN H 194 ASN A 188 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066968 restraints weight = 14561.437| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.66 r_work: 0.2730 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.239 Angle : 0.554 6.034 12041 Z= 0.303 Chirality : 0.042 0.139 1385 Planarity : 0.005 0.062 1511 Dihedral : 4.837 31.260 1225 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.72 % Allowed : 8.49 % Favored : 89.80 % 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: 0.90 (0.25), residues: 1106 helix: 1.57 (0.26), residues: 393 sheet: 0.68 (0.30), residues: 282 loop : -0.30 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7970 (mttm) REVERT: B 217 MET cc_start: 0.8562 (pmm) cc_final: 0.8254 (pmt) REVERT: G 15 LEU cc_start: 0.8243 (tt) cc_final: 0.7965 (tm) REVERT: H 43 LYS cc_start: 0.8692 (mmmm) cc_final: 0.8481 (mmtm) REVERT: H 186 GLN cc_start: 0.9213 (tt0) cc_final: 0.8804 (tt0) REVERT: A 207 GLU cc_start: 0.8494 (tp30) cc_final: 0.8292 (tp30) REVERT: A 306 GLN cc_start: 0.8936 (mm110) cc_final: 0.8353 (mp10) REVERT: A 308 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8538 (mt-10) outliers start: 16 outliers final: 3 residues processed: 134 average time/residue: 1.6612 time to fit residues: 233.5614 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.066863 restraints weight = 14798.841| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.69 r_work: 0.2727 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.239 Angle : 0.554 6.034 12041 Z= 0.303 Chirality : 0.042 0.139 1385 Planarity : 0.005 0.062 1511 Dihedral : 4.837 31.260 1225 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.43 % Allowed : 11.49 % Favored : 88.08 % 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: 0.90 (0.25), residues: 1106 helix: 1.57 (0.26), residues: 393 sheet: 0.68 (0.30), residues: 282 loop : -0.30 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7968 (mttm) REVERT: B 217 MET cc_start: 0.8564 (pmm) cc_final: 0.8264 (pmt) REVERT: G 15 LEU cc_start: 0.8236 (tt) cc_final: 0.7963 (tm) REVERT: H 43 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8475 (mmtm) REVERT: H 186 GLN cc_start: 0.9211 (tt0) cc_final: 0.8800 (tt0) REVERT: A 306 GLN cc_start: 0.8906 (mm110) cc_final: 0.8349 (mp10) outliers start: 4 outliers final: 3 residues processed: 115 average time/residue: 1.6451 time to fit residues: 199.4546 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.066802 restraints weight = 14763.106| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.69 r_work: 0.2727 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.239 Angle : 0.554 6.034 12041 Z= 0.303 Chirality : 0.042 0.139 1385 Planarity : 0.005 0.062 1511 Dihedral : 4.837 31.260 1225 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.43 % Allowed : 11.49 % Favored : 88.08 % 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: 0.90 (0.25), residues: 1106 helix: 1.57 (0.26), residues: 393 sheet: 0.68 (0.30), residues: 282 loop : -0.30 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8181 (mmtm) cc_final: 0.7968 (mttm) REVERT: B 217 MET cc_start: 0.8566 (pmm) cc_final: 0.8265 (pmt) REVERT: G 15 LEU cc_start: 0.8237 (tt) cc_final: 0.7964 (tm) REVERT: H 43 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8475 (mmtm) REVERT: H 186 GLN cc_start: 0.9212 (tt0) cc_final: 0.8801 (tt0) REVERT: A 306 GLN cc_start: 0.8906 (mm110) cc_final: 0.8349 (mp10) outliers start: 4 outliers final: 3 residues processed: 115 average time/residue: 1.6772 time to fit residues: 202.5473 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066944 restraints weight = 14680.968| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.67 r_work: 0.2728 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8865 Z= 0.239 Angle : 0.554 6.034 12041 Z= 0.303 Chirality : 0.042 0.139 1385 Planarity : 0.005 0.062 1511 Dihedral : 4.837 31.260 1225 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.43 % Allowed : 11.49 % Favored : 88.08 % 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: 0.90 (0.25), residues: 1106 helix: 1.57 (0.26), residues: 393 sheet: 0.68 (0.30), residues: 282 loop : -0.30 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.015 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.007 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: R 136 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7968 (mttm) REVERT: B 217 MET cc_start: 0.8563 (pmm) cc_final: 0.8262 (pmt) REVERT: G 15 LEU cc_start: 0.8236 (tt) cc_final: 0.7963 (tm) REVERT: H 43 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8476 (mmtm) REVERT: H 186 GLN cc_start: 0.9211 (tt0) cc_final: 0.8800 (tt0) REVERT: A 306 GLN cc_start: 0.8906 (mm110) cc_final: 0.8349 (mp10) outliers start: 4 outliers final: 3 residues processed: 115 average time/residue: 1.6055 time to fit residues: 194.2499 Evaluate side-chains 115 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 68 optimal weight: 0.0980 chunk 81 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 122 ASN R 172 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.066815 restraints weight = 14582.897| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.64 r_work: 0.2727 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8865 Z= 0.218 Angle : 0.544 6.794 12041 Z= 0.294 Chirality : 0.042 0.135 1385 Planarity : 0.004 0.049 1511 Dihedral : 4.630 22.069 1225 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.50 % Allowed : 10.42 % Favored : 88.08 % 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: 1.19 (0.25), residues: 1106 helix: 1.89 (0.26), residues: 395 sheet: 0.69 (0.30), residues: 287 loop : -0.11 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.010 0.001 HIS A 188 PHE 0.015 0.001 PHE R 189 TYR 0.015 0.001 TYR H 190 ARG 0.008 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: R 111 LEU cc_start: 0.7723 (tp) cc_final: 0.7518 (tm) REVERT: R 127 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8613 (p) REVERT: R 136 LYS cc_start: 0.8178 (mmtm) cc_final: 0.7957 (mttm) REVERT: B 172 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 217 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8324 (pmt) REVERT: B 266 HIS cc_start: 0.8913 (t-90) cc_final: 0.8618 (t-170) REVERT: B 268 ASN cc_start: 0.8993 (m110) cc_final: 0.8758 (p0) REVERT: G 15 LEU cc_start: 0.8311 (tt) cc_final: 0.8020 (tm) REVERT: H 186 GLN cc_start: 0.9219 (tt0) cc_final: 0.8823 (tt0) REVERT: A 306 GLN cc_start: 0.8899 (mm110) cc_final: 0.8347 (mp10) outliers start: 14 outliers final: 4 residues processed: 129 average time/residue: 1.6305 time to fit residues: 221.5471 Evaluate side-chains 120 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 84 PHE Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 432 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain A residue 305 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4202 > 50: distance: 4 - 33: 30.855 distance: 12 - 44: 27.195 distance: 20 - 50: 32.661 distance: 23 - 33: 27.102 distance: 24 - 57: 31.536 distance: 33 - 34: 31.345 distance: 34 - 35: 19.163 distance: 34 - 37: 55.246 distance: 35 - 36: 39.361 distance: 35 - 44: 63.995 distance: 36 - 64: 58.276 distance: 37 - 38: 28.193 distance: 38 - 39: 39.793 distance: 38 - 40: 35.942 distance: 39 - 41: 13.484 distance: 40 - 42: 7.235 distance: 41 - 43: 13.684 distance: 42 - 43: 31.876 distance: 44 - 45: 27.123 distance: 48 - 49: 32.244 distance: 51 - 54: 55.967 distance: 52 - 57: 42.300 distance: 54 - 55: 41.339 distance: 57 - 58: 18.995 distance: 58 - 59: 7.997 distance: 58 - 61: 51.951 distance: 59 - 60: 39.576 distance: 61 - 62: 12.032 distance: 61 - 63: 26.805 distance: 65 - 66: 21.733 distance: 66 - 67: 20.145 distance: 66 - 73: 44.864 distance: 69 - 70: 4.123 distance: 70 - 71: 44.010 distance: 71 - 72: 32.906 distance: 73 - 74: 56.028 distance: 73 - 79: 38.759 distance: 74 - 75: 41.238 distance: 74 - 77: 40.753 distance: 75 - 80: 28.067 distance: 80 - 81: 29.416 distance: 81 - 82: 40.790 distance: 81 - 84: 37.976 distance: 82 - 83: 34.165 distance: 82 - 88: 48.442 distance: 85 - 86: 40.460 distance: 85 - 87: 40.565 distance: 88 - 89: 63.504 distance: 89 - 90: 40.647 distance: 89 - 92: 38.676 distance: 90 - 91: 43.408 distance: 92 - 93: 37.860 distance: 92 - 94: 40.961 distance: 96 - 97: 5.423 distance: 96 - 99: 26.909 distance: 97 - 98: 6.752 distance: 97 - 107: 34.963 distance: 99 - 100: 16.293 distance: 100 - 101: 6.566 distance: 100 - 102: 7.848 distance: 102 - 104: 11.459 distance: 103 - 105: 18.354 distance: 104 - 105: 8.479 distance: 105 - 106: 16.534 distance: 107 - 113: 40.540 distance: 108 - 109: 26.515 distance: 108 - 111: 40.064 distance: 109 - 110: 26.706 distance: 109 - 114: 30.328 distance: 111 - 112: 40.127 distance: 112 - 113: 38.861