Starting phenix.real_space_refine on Wed Jul 30 11:51:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dmp_30766/07_2025/7dmp_30766.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dmp_30766/07_2025/7dmp_30766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dmp_30766/07_2025/7dmp_30766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dmp_30766/07_2025/7dmp_30766.map" model { file = "/net/cci-nas-00/data/ceres_data/7dmp_30766/07_2025/7dmp_30766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dmp_30766/07_2025/7dmp_30766.cif" } resolution = 3.2 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= 0.001 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 38 5.16 5 C 7866 2.51 5 N 2090 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12308 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2704 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 31, 'TRANS': 304} Chain breaks: 4 Chain: "b" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2704 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 31, 'TRANS': 304} Chain breaks: 4 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1521 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "a" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1521 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 4, 'TRANS': 181} Chain: "C" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 2 Chain: "c" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 2 Time building chain proxies: 8.32, per 1000 atoms: 0.68 Number of scatterers: 12308 At special positions: 0 Unit cell: (110.16, 84.66, 223.38, 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 38 16.00 O 2314 8.00 N 2090 7.00 C 7866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 17.1% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'B' and resid 277 through 291 removed outlier: 3.720A pdb=" N GLU B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.652A pdb=" N TYR B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.576A pdb=" N ASP B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 492 removed outlier: 3.769A pdb=" N ARG B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 538 removed outlier: 3.551A pdb=" N LEU B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 removed outlier: 3.963A pdb=" N GLU B 598 " --> pdb=" O PRO B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 688 removed outlier: 3.542A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 285 removed outlier: 3.551A pdb=" N THR b 285 " --> pdb=" O GLU b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 286 through 289 Processing helix chain 'b' and resid 314 through 325 Processing helix chain 'b' and resid 334 through 345 Processing helix chain 'b' and resid 479 through 494 removed outlier: 3.589A pdb=" N LEU b 483 " --> pdb=" O GLU b 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 533 through 538 removed outlier: 3.647A pdb=" N SER b 538 " --> pdb=" O ASP b 534 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 599 removed outlier: 4.077A pdb=" N GLU b 598 " --> pdb=" O PRO b 595 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP b 599 " --> pdb=" O ILE b 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 595 through 599' Processing helix chain 'b' and resid 683 through 690 removed outlier: 3.561A pdb=" N PHE b 690 " --> pdb=" O GLU b 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 24 through 39 removed outlier: 4.150A pdb=" N MET C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 removed outlier: 3.785A pdb=" N ALA C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 135 through 149 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.580A pdb=" N GLU C 180 " --> pdb=" O PRO C 177 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 181 " --> pdb=" O LEU C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'c' and resid 24 through 39 removed outlier: 3.504A pdb=" N LEU c 28 " --> pdb=" O ARG c 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET c 33 " --> pdb=" O LEU c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 68 removed outlier: 4.050A pdb=" N GLN c 67 " --> pdb=" O SER c 64 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU c 68 " --> pdb=" O GLU c 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 64 through 68' Processing helix chain 'c' and resid 89 through 96 removed outlier: 3.912A pdb=" N ILE c 96 " --> pdb=" O MET c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 136 through 151 Processing helix chain 'c' and resid 183 through 187 removed outlier: 3.627A pdb=" N SER c 186 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 276 Processing sheet with id=AA1, first strand: chain 'B' and resid 441 through 442 removed outlier: 5.839A pdb=" N GLU B 369 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N PHE B 354 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TRP B 355 " --> pdb=" O ASN B 644 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 637 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 623 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 496 through 498 Processing sheet with id=AA3, first strand: chain 'b' and resid 441 through 442 removed outlier: 3.614A pdb=" N PHE b 431 " --> pdb=" O ALA b 368 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU b 369 " --> pdb=" O PHE b 354 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE b 354 " --> pdb=" O GLU b 369 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU b 371 " --> pdb=" O CYS b 352 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS b 352 " --> pdb=" O GLU b 371 " (cutoff:3.500A) removed outlier: 15.264A pdb=" N PHE b 642 " --> pdb=" O ARG b 351 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ARG b 353 " --> pdb=" O PHE b 642 " (cutoff:3.500A) removed outlier: 9.937A pdb=" N ASN b 644 " --> pdb=" O ARG b 353 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TRP b 355 " --> pdb=" O ASN b 644 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR b 646 " --> pdb=" O TRP b 355 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ALA b 633 " --> pdb=" O SER b 627 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 497 through 498 Processing sheet with id=AA5, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.854A pdb=" N GLN A 56 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 49 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 54 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 79 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 72 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 77 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 89 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 104 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A 91 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 102 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 93 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 114 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 127 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 116 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 125 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.854A pdb=" N GLN A 56 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A 49 " --> pdb=" O HIS A 54 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N HIS A 54 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLN A 79 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 72 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS A 77 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 89 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 104 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU A 91 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN A 102 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU A 93 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 114 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR A 127 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU A 116 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 125 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU A 197 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 37 removed outlier: 3.574A pdb=" N SER a 47 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN a 56 " --> pdb=" O SER a 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 49 " --> pdb=" O HIS a 54 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS a 54 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN a 79 " --> pdb=" O ASP a 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL a 72 " --> pdb=" O HIS a 77 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS a 77 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN a 102 " --> pdb=" O GLU a 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA a 95 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS a 100 " --> pdb=" O ALA a 95 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN a 125 " --> pdb=" O GLU a 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 34 through 37 removed outlier: 3.574A pdb=" N SER a 47 " --> pdb=" O GLN a 56 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN a 56 " --> pdb=" O SER a 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU a 49 " --> pdb=" O HIS a 54 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS a 54 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN a 79 " --> pdb=" O ASP a 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL a 72 " --> pdb=" O HIS a 77 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N HIS a 77 " --> pdb=" O VAL a 72 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLN a 102 " --> pdb=" O GLU a 93 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ALA a 95 " --> pdb=" O HIS a 100 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS a 100 " --> pdb=" O ALA a 95 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN a 125 " --> pdb=" O GLU a 116 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS a 180 " --> pdb=" O PHE a 176 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU a 181 " --> pdb=" O GLU a 198 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU a 198 " --> pdb=" O GLU a 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 163 through 164 Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 48 removed outlier: 6.670A pdb=" N ILE C 59 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 72 " --> pdb=" O GLY C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR C 75 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER C 83 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'C' and resid 226 through 230 removed outlier: 5.109A pdb=" N LEU C 247 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 43 through 48 removed outlier: 5.442A pdb=" N VAL c 44 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU c 63 " --> pdb=" O VAL c 44 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE c 46 " --> pdb=" O GLN c 61 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN c 61 " --> pdb=" O PHE c 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 110 through 113 Processing sheet with id=AB6, first strand: chain 'c' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'c' and resid 226 through 230 removed outlier: 4.815A pdb=" N LEU c 247 " --> pdb=" O SER c 241 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1203 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: 5.05 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3461 1.33 - 1.45: 2386 1.45 - 1.57: 6734 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 12646 Sorted by residual: bond pdb=" C ILE C 221 " pdb=" N PRO C 222 " ideal model delta sigma weight residual 1.332 1.372 -0.040 8.20e-03 1.49e+04 2.38e+01 bond pdb=" C ILE c 221 " pdb=" N PRO c 222 " ideal model delta sigma weight residual 1.337 1.376 -0.039 1.24e-02 6.50e+03 9.85e+00 bond pdb=" C TRP b 630 " pdb=" O TRP b 630 " ideal model delta sigma weight residual 1.246 1.225 0.021 9.20e-03 1.18e+04 5.37e+00 bond pdb=" C VAL B 314 " pdb=" O VAL B 314 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.17e-02 7.31e+03 4.17e+00 bond pdb=" C SER c 21 " pdb=" N PRO c 22 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.82e+00 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 16583 1.83 - 3.65: 467 3.65 - 5.48: 65 5.48 - 7.31: 25 7.31 - 9.14: 12 Bond angle restraints: 17152 Sorted by residual: angle pdb=" N VAL a 27 " pdb=" CA VAL a 27 " pdb=" C VAL a 27 " ideal model delta sigma weight residual 113.71 109.11 4.60 9.50e-01 1.11e+00 2.34e+01 angle pdb=" C ALA a 95 " pdb=" N ASP a 96 " pdb=" CA ASP a 96 " ideal model delta sigma weight residual 121.54 130.68 -9.14 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C ILE b 617 " pdb=" N PRO b 618 " pdb=" CA PRO b 618 " ideal model delta sigma weight residual 119.05 124.17 -5.12 1.11e+00 8.12e-01 2.13e+01 angle pdb=" C ASN B 478 " pdb=" N GLU B 479 " pdb=" CA GLU B 479 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.89e+01 angle pdb=" N TYR b 620 " pdb=" CA TYR b 620 " pdb=" C TYR b 620 " ideal model delta sigma weight residual 109.11 115.08 -5.97 1.42e+00 4.96e-01 1.77e+01 ... (remaining 17147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6672 18.01 - 36.01: 603 36.01 - 54.02: 100 54.02 - 72.03: 29 72.03 - 90.03: 22 Dihedral angle restraints: 7426 sinusoidal: 3038 harmonic: 4388 Sorted by residual: dihedral pdb=" CA SER C 21 " pdb=" C SER C 21 " pdb=" N PRO C 22 " pdb=" CA PRO C 22 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C ASN a 165 " pdb=" N ASN a 165 " pdb=" CA ASN a 165 " pdb=" CB ASN a 165 " ideal model delta harmonic sigma weight residual -122.60 -133.48 10.88 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" CA PRO C 22 " pdb=" C PRO C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1502 0.072 - 0.144: 244 0.144 - 0.217: 16 0.217 - 0.289: 3 0.289 - 0.361: 1 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ASN a 165 " pdb=" N ASN a 165 " pdb=" C ASN a 165 " pdb=" CB ASN a 165 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA LYS a 166 " pdb=" N LYS a 166 " pdb=" C LYS a 166 " pdb=" CB LYS a 166 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASP a 96 " pdb=" N ASP a 96 " pdb=" C ASP a 96 " pdb=" CB ASP a 96 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1763 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 435 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 436 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 436 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 436 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA c 69 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO c 70 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO c 70 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO c 70 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 21 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO c 22 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO c 22 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO c 22 " 0.030 5.00e-02 4.00e+02 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 1 1.80 - 2.57: 111 2.57 - 3.35: 14164 3.35 - 4.12: 31027 4.12 - 4.90: 55617 Nonbonded interactions: 100920 Sorted by model distance: nonbonded pdb=" OH TYR b 634 " pdb=" CG GLN c 18 " model vdw 1.020 3.440 nonbonded pdb=" OH TYR b 634 " pdb=" CD GLN c 18 " model vdw 1.948 3.270 nonbonded pdb=" OD1 ASN b 615 " pdb=" OD2 ASP c 23 " model vdw 1.987 3.040 nonbonded pdb=" CG2 VAL b 326 " pdb=" CE1 TYR b 634 " model vdw 2.052 3.760 nonbonded pdb=" OE2 GLU B 316 " pdb=" NZ LYS B 641 " model vdw 2.119 3.120 ... (remaining 100915 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } 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: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.130 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 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 : 0.003 0.046 12646 Z= 0.190 Angle : 0.758 9.135 17152 Z= 0.438 Chirality : 0.052 0.361 1766 Planarity : 0.006 0.060 2248 Dihedral : 14.924 90.032 4646 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.61 % Allowed : 7.12 % Favored : 91.27 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.17), residues: 1492 helix: -3.09 (0.24), residues: 218 sheet: -2.68 (0.23), residues: 372 loop : -3.01 (0.16), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 542 HIS 0.004 0.001 HIS A 120 PHE 0.015 0.001 PHE B 636 TYR 0.014 0.001 TYR b 334 ARG 0.002 0.000 ARG b 484 Details of bonding type rmsd hydrogen bonds : bond 0.16127 ( 363) hydrogen bonds : angle 8.03617 ( 1203) covalent geometry : bond 0.00334 (12646) covalent geometry : angle 0.75772 (17152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 351 ARG cc_start: 0.6407 (ttp80) cc_final: 0.5807 (ttp80) REVERT: b 619 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5829 (tt0) REVERT: A 89 ARG cc_start: 0.8233 (ptt90) cc_final: 0.7690 (ptt-90) REVERT: A 102 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7204 (mm110) REVERT: A 155 LEU cc_start: 0.8164 (mt) cc_final: 0.7933 (mt) REVERT: a 109 ASN cc_start: 0.8196 (p0) cc_final: 0.7904 (p0) REVERT: a 110 ASN cc_start: 0.6173 (t0) cc_final: 0.5917 (t0) REVERT: a 164 MET cc_start: 0.7802 (mmm) cc_final: 0.7601 (mmm) REVERT: C 20 LEU cc_start: 0.6258 (mt) cc_final: 0.5969 (mt) REVERT: C 270 MET cc_start: 0.5713 (mmt) cc_final: 0.5376 (mmt) REVERT: c 94 MET cc_start: 0.6583 (ptp) cc_final: 0.6109 (mtm) REVERT: c 104 MET cc_start: 0.7583 (tpt) cc_final: 0.7337 (tpp) REVERT: c 134 ILE cc_start: 0.6809 (tp) cc_final: 0.6397 (tp) REVERT: c 230 MET cc_start: 0.6623 (mmm) cc_final: 0.6269 (mmt) REVERT: c 270 MET cc_start: 0.5249 (mmm) cc_final: 0.4925 (mmm) outliers start: 21 outliers final: 12 residues processed: 314 average time/residue: 0.2938 time to fit residues: 125.0221 Evaluate side-chains 203 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain b residue 310 SER Chi-restraints excluded: chain b residue 612 LEU Chi-restraints excluded: chain b residue 619 GLN Chi-restraints excluded: chain b residue 622 ILE Chi-restraints excluded: chain b residue 625 LEU Chi-restraints excluded: chain b residue 627 SER Chi-restraints excluded: chain b residue 636 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 HIS B 541 ASN b 478 ASN ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 619 GLN ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS A 110 ASN ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 HIS A 160 GLN a 31 HIS a 123 HIS ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 189 HIS c 251 HIS c 257 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.140152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109015 restraints weight = 18494.695| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.84 r_work: 0.3493 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12646 Z= 0.301 Angle : 0.744 8.291 17152 Z= 0.387 Chirality : 0.048 0.192 1766 Planarity : 0.006 0.046 2248 Dihedral : 6.311 59.167 1717 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.45 % Allowed : 14.40 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.18), residues: 1492 helix: -1.76 (0.29), residues: 224 sheet: -2.72 (0.23), residues: 368 loop : -2.62 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 141 HIS 0.007 0.002 HIS a 120 PHE 0.020 0.003 PHE b 645 TYR 0.022 0.002 TYR C 262 ARG 0.007 0.001 ARG b 438 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 363) hydrogen bonds : angle 6.27681 ( 1203) covalent geometry : bond 0.00647 (12646) covalent geometry : angle 0.74410 (17152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 362 GLU cc_start: 0.7283 (pm20) cc_final: 0.7007 (pm20) REVERT: A 66 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7532 (mtp-110) REVERT: A 185 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6908 (tm-30) REVERT: a 37 ARG cc_start: 0.7537 (ttm110) cc_final: 0.6629 (mtm110) REVERT: a 38 LEU cc_start: 0.7671 (mm) cc_final: 0.7030 (mp) REVERT: a 109 ASN cc_start: 0.8245 (p0) cc_final: 0.7649 (p0) REVERT: a 111 ASP cc_start: 0.7942 (m-30) cc_final: 0.7653 (m-30) REVERT: c 94 MET cc_start: 0.7329 (ptp) cc_final: 0.6609 (mtm) REVERT: c 170 ASN cc_start: 0.6879 (t0) cc_final: 0.6626 (t0) REVERT: c 230 MET cc_start: 0.7731 (mmm) cc_final: 0.7404 (mmt) REVERT: c 250 TYR cc_start: 0.7434 (p90) cc_final: 0.6680 (p90) outliers start: 32 outliers final: 16 residues processed: 241 average time/residue: 0.2662 time to fit residues: 90.1208 Evaluate side-chains 199 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain b residue 478 ASN Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 136 GLU Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 217 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 64 optimal weight: 0.0870 chunk 146 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 495 HIS ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 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 = 0.4046 r_free = 0.4046 target = 0.139910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109111 restraints weight = 18839.907| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.85 r_work: 0.3493 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12646 Z= 0.155 Angle : 0.609 9.118 17152 Z= 0.309 Chirality : 0.044 0.162 1766 Planarity : 0.004 0.041 2248 Dihedral : 4.587 21.264 1692 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.53 % Allowed : 16.92 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.19), residues: 1492 helix: -1.04 (0.33), residues: 222 sheet: -2.53 (0.25), residues: 348 loop : -2.32 (0.18), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 440 HIS 0.010 0.001 HIS b 545 PHE 0.024 0.002 PHE C 46 TYR 0.018 0.002 TYR B 365 ARG 0.006 0.000 ARG b 438 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 363) hydrogen bonds : angle 5.87739 ( 1203) covalent geometry : bond 0.00347 (12646) covalent geometry : angle 0.60878 (17152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 362 GLU cc_start: 0.7213 (pm20) cc_final: 0.6991 (pm20) REVERT: A 42 ASP cc_start: 0.5589 (m-30) cc_final: 0.5205 (m-30) REVERT: A 185 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6927 (tm-30) REVERT: a 37 ARG cc_start: 0.7529 (ttm110) cc_final: 0.6405 (mtm110) REVERT: a 38 LEU cc_start: 0.7581 (mm) cc_final: 0.6931 (mp) REVERT: a 109 ASN cc_start: 0.8287 (p0) cc_final: 0.7616 (p0) REVERT: a 111 ASP cc_start: 0.7919 (m-30) cc_final: 0.7585 (m-30) REVERT: C 32 LEU cc_start: 0.7806 (mt) cc_final: 0.7606 (mt) REVERT: C 188 PHE cc_start: 0.7185 (m-10) cc_final: 0.6888 (m-10) REVERT: c 94 MET cc_start: 0.7359 (ptp) cc_final: 0.6790 (mtm) REVERT: c 149 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7170 (mmtm) REVERT: c 230 MET cc_start: 0.7594 (mmm) cc_final: 0.7313 (mmt) REVERT: c 250 TYR cc_start: 0.7402 (p90) cc_final: 0.6563 (p90) outliers start: 33 outliers final: 21 residues processed: 235 average time/residue: 0.2671 time to fit residues: 88.9673 Evaluate side-chains 210 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 95 GLN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 0 optimal weight: 3.9990 chunk 117 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 138 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 0.0870 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 544 HIS ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.138973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108446 restraints weight = 18638.012| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.82 r_work: 0.3483 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12646 Z= 0.149 Angle : 0.590 8.396 17152 Z= 0.301 Chirality : 0.044 0.166 1766 Planarity : 0.004 0.041 2248 Dihedral : 4.476 20.847 1692 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.45 % Allowed : 17.00 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.20), residues: 1492 helix: -0.93 (0.33), residues: 234 sheet: -2.51 (0.25), residues: 346 loop : -2.17 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.007 0.001 HIS b 545 PHE 0.016 0.001 PHE C 46 TYR 0.016 0.001 TYR B 365 ARG 0.005 0.000 ARG b 438 Details of bonding type rmsd hydrogen bonds : bond 0.03102 ( 363) hydrogen bonds : angle 5.69667 ( 1203) covalent geometry : bond 0.00335 (12646) covalent geometry : angle 0.59033 (17152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 1.315 Fit side-chains REVERT: B 362 GLU cc_start: 0.7295 (pm20) cc_final: 0.6997 (pm20) REVERT: B 366 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 37 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7268 (ttp-110) REVERT: A 66 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7617 (mtp-110) REVERT: A 185 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6834 (tm-30) REVERT: a 37 ARG cc_start: 0.7498 (ttm110) cc_final: 0.6392 (mtm110) REVERT: a 38 LEU cc_start: 0.7615 (mm) cc_final: 0.6960 (mp) REVERT: a 109 ASN cc_start: 0.8320 (p0) cc_final: 0.7652 (p0) REVERT: a 111 ASP cc_start: 0.7941 (m-30) cc_final: 0.7687 (m-30) REVERT: C 32 LEU cc_start: 0.7813 (mt) cc_final: 0.7596 (mt) REVERT: C 188 PHE cc_start: 0.7219 (m-10) cc_final: 0.6946 (m-10) REVERT: c 92 MET cc_start: 0.7649 (ptm) cc_final: 0.7313 (ttp) REVERT: c 94 MET cc_start: 0.7377 (ptp) cc_final: 0.6826 (mtm) REVERT: c 135 LYS cc_start: 0.7572 (tptt) cc_final: 0.7304 (mmmt) REVERT: c 149 LYS cc_start: 0.7646 (mmmt) cc_final: 0.7303 (mmtm) REVERT: c 230 MET cc_start: 0.7529 (mmm) cc_final: 0.7247 (mmt) REVERT: c 250 TYR cc_start: 0.7395 (p90) cc_final: 0.6522 (p90) REVERT: c 270 MET cc_start: 0.6940 (mmm) cc_final: 0.6477 (mmm) outliers start: 45 outliers final: 32 residues processed: 231 average time/residue: 0.2651 time to fit residues: 86.5257 Evaluate side-chains 218 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 331 ASP Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 457 ILE Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 HIS ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 680 ASN A 125 GLN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.133028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102239 restraints weight = 18850.255| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.78 r_work: 0.3374 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12646 Z= 0.234 Angle : 0.667 10.268 17152 Z= 0.340 Chirality : 0.046 0.211 1766 Planarity : 0.005 0.043 2248 Dihedral : 4.810 21.784 1692 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.75 % Allowed : 17.38 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.20), residues: 1492 helix: -1.25 (0.31), residues: 250 sheet: -2.61 (0.25), residues: 338 loop : -2.09 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 117 HIS 0.031 0.002 HIS b 544 PHE 0.020 0.002 PHE B 558 TYR 0.019 0.002 TYR B 365 ARG 0.008 0.001 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 363) hydrogen bonds : angle 5.88023 ( 1203) covalent geometry : bond 0.00527 (12646) covalent geometry : angle 0.66673 (17152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 1.468 Fit side-chains REVERT: B 366 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8414 (mp) REVERT: A 37 ARG cc_start: 0.7581 (ttm110) cc_final: 0.7244 (ttp-110) REVERT: A 66 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7499 (mtp-110) REVERT: A 155 LEU cc_start: 0.8162 (mp) cc_final: 0.7792 (mp) REVERT: A 185 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7057 (tm-30) REVERT: a 37 ARG cc_start: 0.7477 (ttm110) cc_final: 0.6584 (mtm110) REVERT: a 38 LEU cc_start: 0.7537 (mm) cc_final: 0.6892 (mp) REVERT: a 109 ASN cc_start: 0.8388 (p0) cc_final: 0.7633 (p0) REVERT: a 111 ASP cc_start: 0.8079 (m-30) cc_final: 0.7705 (m-30) REVERT: a 113 TYR cc_start: 0.7294 (t80) cc_final: 0.7082 (t80) REVERT: C 168 HIS cc_start: 0.7098 (m170) cc_final: 0.6837 (m-70) REVERT: C 223 ARG cc_start: 0.7456 (ppt170) cc_final: 0.7218 (ttm-80) REVERT: C 262 TYR cc_start: 0.8606 (t80) cc_final: 0.8207 (t80) REVERT: c 29 LEU cc_start: 0.8484 (mm) cc_final: 0.8196 (mm) REVERT: c 92 MET cc_start: 0.7798 (ptm) cc_final: 0.7440 (ttp) REVERT: c 94 MET cc_start: 0.7481 (ptp) cc_final: 0.6880 (mtm) REVERT: c 135 LYS cc_start: 0.7701 (tptt) cc_final: 0.7467 (mmmt) REVERT: c 149 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7483 (mmtm) REVERT: c 230 MET cc_start: 0.7828 (mmm) cc_final: 0.7548 (mmt) REVERT: c 250 TYR cc_start: 0.7473 (p90) cc_final: 0.6578 (p90) REVERT: c 270 MET cc_start: 0.6973 (mmm) cc_final: 0.6684 (mmm) outliers start: 49 outliers final: 38 residues processed: 232 average time/residue: 0.2726 time to fit residues: 90.3091 Evaluate side-chains 222 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 469 VAL Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 545 HIS Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain c residue 45 LEU Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 214 LEU Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.0040 chunk 12 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 0.0980 chunk 102 optimal weight: 0.0070 chunk 86 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 overall best weight: 0.1010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.138305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108010 restraints weight = 18848.744| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.82 r_work: 0.3466 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12646 Z= 0.115 Angle : 0.595 8.529 17152 Z= 0.301 Chirality : 0.044 0.160 1766 Planarity : 0.004 0.039 2248 Dihedral : 4.520 20.596 1692 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.14 % Allowed : 18.76 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.20), residues: 1492 helix: -0.74 (0.33), residues: 238 sheet: -2.49 (0.25), residues: 340 loop : -1.97 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.020 0.001 HIS a 31 PHE 0.018 0.001 PHE B 558 TYR 0.024 0.001 TYR C 258 ARG 0.006 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 363) hydrogen bonds : angle 5.55811 ( 1203) covalent geometry : bond 0.00252 (12646) covalent geometry : angle 0.59506 (17152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: B 366 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8373 (mp) REVERT: b 441 VAL cc_start: 0.8571 (t) cc_final: 0.8319 (m) REVERT: A 37 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7117 (ttp-110) REVERT: A 66 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7464 (mtp-110) REVERT: A 155 LEU cc_start: 0.8143 (mp) cc_final: 0.7849 (mp) REVERT: A 185 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6976 (tm-30) REVERT: a 37 ARG cc_start: 0.7458 (ttm110) cc_final: 0.6796 (ttp-110) REVERT: a 38 LEU cc_start: 0.7455 (mm) cc_final: 0.6878 (mp) REVERT: a 109 ASN cc_start: 0.8423 (p0) cc_final: 0.7824 (p0) REVERT: a 111 ASP cc_start: 0.7944 (m-30) cc_final: 0.7721 (m-30) REVERT: a 195 GLU cc_start: 0.8022 (tt0) cc_final: 0.7279 (tt0) REVERT: C 20 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6299 (mm) REVERT: C 168 HIS cc_start: 0.7004 (m170) cc_final: 0.6721 (m-70) REVERT: C 188 PHE cc_start: 0.7339 (m-10) cc_final: 0.7123 (m-10) REVERT: c 29 LEU cc_start: 0.8446 (mm) cc_final: 0.8212 (mm) REVERT: c 92 MET cc_start: 0.7778 (ptm) cc_final: 0.7554 (ttp) REVERT: c 94 MET cc_start: 0.7472 (ptp) cc_final: 0.6829 (mtm) REVERT: c 135 LYS cc_start: 0.7656 (tptt) cc_final: 0.7410 (mmmt) REVERT: c 149 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7371 (mmtm) REVERT: c 230 MET cc_start: 0.7485 (mmm) cc_final: 0.7225 (mmt) REVERT: c 250 TYR cc_start: 0.7343 (p90) cc_final: 0.6473 (p90) REVERT: c 270 MET cc_start: 0.6766 (mmm) cc_final: 0.6503 (mmm) REVERT: c 272 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7874 (tp) REVERT: c 275 MET cc_start: 0.8697 (mmm) cc_final: 0.8413 (mmt) outliers start: 41 outliers final: 29 residues processed: 231 average time/residue: 0.2694 time to fit residues: 88.7996 Evaluate side-chains 215 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 221 ILE Chi-restraints excluded: chain c residue 272 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 137 optimal weight: 0.0270 chunk 23 optimal weight: 0.0470 chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 147 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 chunk 78 optimal weight: 0.8980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.138361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108138 restraints weight = 18659.863| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.81 r_work: 0.3470 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12646 Z= 0.118 Angle : 0.590 8.952 17152 Z= 0.298 Chirality : 0.043 0.165 1766 Planarity : 0.004 0.038 2248 Dihedral : 4.422 19.826 1692 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.22 % Allowed : 19.60 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1492 helix: -0.62 (0.34), residues: 238 sheet: -2.34 (0.25), residues: 360 loop : -1.88 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 82 HIS 0.011 0.001 HIS a 31 PHE 0.017 0.001 PHE B 558 TYR 0.024 0.002 TYR c 262 ARG 0.006 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 363) hydrogen bonds : angle 5.42602 ( 1203) covalent geometry : bond 0.00262 (12646) covalent geometry : angle 0.58971 (17152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 1.317 Fit side-chains REVERT: B 366 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8345 (mp) REVERT: b 441 VAL cc_start: 0.8572 (t) cc_final: 0.8348 (m) REVERT: A 37 ARG cc_start: 0.7514 (ttm110) cc_final: 0.7215 (ttp-110) REVERT: A 66 ARG cc_start: 0.7791 (ttp80) cc_final: 0.7469 (mtp-110) REVERT: A 155 LEU cc_start: 0.8168 (mp) cc_final: 0.7846 (mp) REVERT: A 182 GLN cc_start: 0.7203 (pt0) cc_final: 0.6974 (pt0) REVERT: A 185 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6978 (tm-30) REVERT: a 37 ARG cc_start: 0.7461 (ttm110) cc_final: 0.6631 (mtm110) REVERT: a 38 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6803 (mp) REVERT: a 109 ASN cc_start: 0.8434 (p0) cc_final: 0.7836 (p0) REVERT: a 111 ASP cc_start: 0.7921 (m-30) cc_final: 0.7681 (m-30) REVERT: C 20 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6343 (mm) REVERT: C 168 HIS cc_start: 0.7080 (m170) cc_final: 0.6785 (m90) REVERT: C 188 PHE cc_start: 0.7344 (m-10) cc_final: 0.7138 (m-10) REVERT: c 29 LEU cc_start: 0.8436 (mm) cc_final: 0.8225 (mm) REVERT: c 92 MET cc_start: 0.7747 (ptm) cc_final: 0.7516 (ttp) REVERT: c 94 MET cc_start: 0.7419 (ptp) cc_final: 0.6791 (mtm) REVERT: c 149 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7416 (mmtm) REVERT: c 230 MET cc_start: 0.7510 (mmm) cc_final: 0.7266 (mmt) REVERT: c 250 TYR cc_start: 0.7291 (p90) cc_final: 0.6436 (p90) REVERT: c 272 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7890 (tp) REVERT: c 275 MET cc_start: 0.8732 (mmm) cc_final: 0.8437 (mmt) outliers start: 42 outliers final: 32 residues processed: 225 average time/residue: 0.2707 time to fit residues: 85.9215 Evaluate side-chains 220 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 655 VAL Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 221 ILE Chi-restraints excluded: chain c residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 123 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.134684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104067 restraints weight = 18931.650| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.81 r_work: 0.3408 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12646 Z= 0.179 Angle : 0.638 10.892 17152 Z= 0.321 Chirality : 0.045 0.193 1766 Planarity : 0.004 0.050 2248 Dihedral : 4.573 21.195 1692 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.37 % Allowed : 20.29 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.20), residues: 1492 helix: -0.66 (0.33), residues: 236 sheet: -2.45 (0.25), residues: 350 loop : -1.91 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP c 82 HIS 0.022 0.001 HIS a 31 PHE 0.020 0.002 PHE B 558 TYR 0.029 0.002 TYR A 113 ARG 0.010 0.001 ARG c 171 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 363) hydrogen bonds : angle 5.58045 ( 1203) covalent geometry : bond 0.00407 (12646) covalent geometry : angle 0.63807 (17152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.418 Fit side-chains REVERT: B 366 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8351 (mp) REVERT: A 37 ARG cc_start: 0.7586 (ttm110) cc_final: 0.7322 (ttp-110) REVERT: A 66 ARG cc_start: 0.7825 (ttp80) cc_final: 0.7488 (mtp-110) REVERT: A 155 LEU cc_start: 0.8205 (mp) cc_final: 0.7884 (mp) REVERT: a 37 ARG cc_start: 0.7525 (ttm110) cc_final: 0.6802 (ttp-110) REVERT: a 38 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6931 (mp) REVERT: a 109 ASN cc_start: 0.8408 (p0) cc_final: 0.7685 (p0) REVERT: a 111 ASP cc_start: 0.8060 (m-30) cc_final: 0.7753 (m-30) REVERT: C 20 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6663 (mm) REVERT: C 32 LEU cc_start: 0.7866 (mt) cc_final: 0.7636 (mt) REVERT: C 168 HIS cc_start: 0.7234 (m170) cc_final: 0.6925 (m90) REVERT: c 29 LEU cc_start: 0.8450 (mm) cc_final: 0.8188 (mm) REVERT: c 92 MET cc_start: 0.7799 (ptm) cc_final: 0.7555 (ttp) REVERT: c 94 MET cc_start: 0.7453 (ptp) cc_final: 0.6818 (mtm) REVERT: c 106 ASP cc_start: 0.6929 (t0) cc_final: 0.6396 (t0) REVERT: c 149 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7519 (mmtm) REVERT: c 250 TYR cc_start: 0.7372 (p90) cc_final: 0.6504 (p90) REVERT: c 275 MET cc_start: 0.8751 (mmm) cc_final: 0.8202 (mmt) outliers start: 44 outliers final: 38 residues processed: 221 average time/residue: 0.2748 time to fit residues: 86.8374 Evaluate side-chains 224 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 655 VAL Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 89 THR Chi-restraints excluded: chain c residue 95 GLN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 153 ILE Chi-restraints excluded: chain c residue 221 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 33 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 141 optimal weight: 0.5980 chunk 139 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 133 optimal weight: 0.9980 chunk 83 optimal weight: 0.2980 chunk 93 optimal weight: 1.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105197 restraints weight = 18716.994| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.80 r_work: 0.3429 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12646 Z= 0.145 Angle : 0.619 8.970 17152 Z= 0.312 Chirality : 0.044 0.170 1766 Planarity : 0.004 0.055 2248 Dihedral : 4.541 21.603 1692 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.29 % Allowed : 20.14 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1492 helix: -0.57 (0.34), residues: 236 sheet: -2.43 (0.25), residues: 350 loop : -1.87 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 82 HIS 0.012 0.001 HIS a 31 PHE 0.018 0.001 PHE B 558 TYR 0.020 0.002 TYR B 365 ARG 0.009 0.001 ARG c 171 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 363) hydrogen bonds : angle 5.50910 ( 1203) covalent geometry : bond 0.00329 (12646) covalent geometry : angle 0.61861 (17152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 1.312 Fit side-chains REVERT: B 366 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 619 GLN cc_start: 0.6159 (mt0) cc_final: 0.5843 (tt0) REVERT: A 37 ARG cc_start: 0.7561 (ttm110) cc_final: 0.7306 (ttp-110) REVERT: A 66 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7478 (mtp-110) REVERT: A 155 LEU cc_start: 0.8175 (mp) cc_final: 0.7869 (mp) REVERT: a 37 ARG cc_start: 0.7568 (ttm110) cc_final: 0.6809 (ttp-110) REVERT: a 38 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6875 (mp) REVERT: a 109 ASN cc_start: 0.8414 (p0) cc_final: 0.7685 (p0) REVERT: a 111 ASP cc_start: 0.7984 (m-30) cc_final: 0.7710 (m-30) REVERT: a 187 ARG cc_start: 0.7623 (mmt90) cc_final: 0.7076 (mpt-90) REVERT: C 20 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.6455 (mm) REVERT: C 32 LEU cc_start: 0.7866 (mt) cc_final: 0.7628 (mt) REVERT: C 168 HIS cc_start: 0.7230 (m170) cc_final: 0.6983 (m90) REVERT: c 29 LEU cc_start: 0.8458 (mm) cc_final: 0.8206 (mm) REVERT: c 92 MET cc_start: 0.7698 (ptm) cc_final: 0.7476 (ttp) REVERT: c 94 MET cc_start: 0.7393 (ptp) cc_final: 0.6760 (mtm) REVERT: c 106 ASP cc_start: 0.7025 (t0) cc_final: 0.6553 (t0) REVERT: c 149 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7531 (mmtm) REVERT: c 250 TYR cc_start: 0.7355 (p90) cc_final: 0.6500 (p90) REVERT: c 272 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7984 (tp) REVERT: c 275 MET cc_start: 0.8740 (mmm) cc_final: 0.8376 (mmt) outliers start: 43 outliers final: 35 residues processed: 222 average time/residue: 0.2636 time to fit residues: 83.9480 Evaluate side-chains 221 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 655 VAL Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 95 GLN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 221 ILE Chi-restraints excluded: chain c residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 144 optimal weight: 0.0770 chunk 149 optimal weight: 0.9980 chunk 41 optimal weight: 0.0270 chunk 96 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105233 restraints weight = 18514.030| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.66 r_work: 0.3446 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12646 Z= 0.143 Angle : 0.625 9.721 17152 Z= 0.314 Chirality : 0.044 0.170 1766 Planarity : 0.004 0.041 2248 Dihedral : 4.525 21.236 1692 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.22 % Allowed : 20.29 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.20), residues: 1492 helix: -0.55 (0.34), residues: 236 sheet: -2.39 (0.25), residues: 350 loop : -1.83 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 82 HIS 0.010 0.001 HIS a 31 PHE 0.023 0.002 PHE C 160 TYR 0.021 0.002 TYR A 113 ARG 0.008 0.001 ARG c 171 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 363) hydrogen bonds : angle 5.47680 ( 1203) covalent geometry : bond 0.00325 (12646) covalent geometry : angle 0.62452 (17152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2984 Ramachandran restraints generated. 1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.405 Fit side-chains REVERT: B 366 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 619 GLN cc_start: 0.6154 (mt0) cc_final: 0.5917 (tt0) REVERT: b 441 VAL cc_start: 0.8628 (t) cc_final: 0.8376 (m) REVERT: A 37 ARG cc_start: 0.7563 (ttm110) cc_final: 0.7325 (ttp-110) REVERT: A 66 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7478 (mtp-110) REVERT: A 155 LEU cc_start: 0.8172 (mp) cc_final: 0.7863 (mp) REVERT: a 37 ARG cc_start: 0.7591 (ttm110) cc_final: 0.6947 (ttp-110) REVERT: a 38 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6903 (mp) REVERT: a 109 ASN cc_start: 0.8447 (p0) cc_final: 0.7793 (p0) REVERT: a 111 ASP cc_start: 0.8002 (m-30) cc_final: 0.7724 (m-30) REVERT: a 187 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7163 (mpt-90) REVERT: a 195 GLU cc_start: 0.7853 (tt0) cc_final: 0.7596 (tt0) REVERT: C 20 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6493 (mm) REVERT: C 32 LEU cc_start: 0.7862 (mt) cc_final: 0.7619 (mt) REVERT: C 168 HIS cc_start: 0.7252 (m170) cc_final: 0.7041 (m90) REVERT: c 29 LEU cc_start: 0.8465 (mm) cc_final: 0.8241 (mm) REVERT: c 92 MET cc_start: 0.7637 (ptm) cc_final: 0.7410 (ttp) REVERT: c 106 ASP cc_start: 0.7002 (t0) cc_final: 0.6560 (t0) REVERT: c 149 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7526 (mmtm) REVERT: c 272 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7915 (tp) REVERT: c 275 MET cc_start: 0.8752 (mmm) cc_final: 0.8179 (mmt) outliers start: 42 outliers final: 36 residues processed: 214 average time/residue: 0.2495 time to fit residues: 76.3830 Evaluate side-chains 222 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain b residue 316 GLU Chi-restraints excluded: chain b residue 370 VAL Chi-restraints excluded: chain b residue 447 THR Chi-restraints excluded: chain b residue 501 PHE Chi-restraints excluded: chain b residue 544 HIS Chi-restraints excluded: chain b residue 588 VAL Chi-restraints excluded: chain b residue 655 VAL Chi-restraints excluded: chain b residue 692 MET Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 74 ASN Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain a residue 31 HIS Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 114 THR Chi-restraints excluded: chain a residue 185 GLU Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 95 GLN Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain c residue 132 VAL Chi-restraints excluded: chain c residue 221 ILE Chi-restraints excluded: chain c residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 90 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 31 HIS a 110 ASN ** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.134097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103661 restraints weight = 18694.928| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.78 r_work: 0.3405 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12646 Z= 0.174 Angle : 0.640 9.367 17152 Z= 0.322 Chirality : 0.045 0.171 1766 Planarity : 0.004 0.041 2248 Dihedral : 4.590 21.523 1692 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.29 % Allowed : 20.44 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.20), residues: 1492 helix: -0.58 (0.33), residues: 236 sheet: -2.38 (0.25), residues: 350 loop : -1.83 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 82 HIS 0.017 0.001 HIS a 31 PHE 0.022 0.002 PHE C 188 TYR 0.020 0.002 TYR A 113 ARG 0.008 0.001 ARG c 171 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 363) hydrogen bonds : angle 5.53619 ( 1203) covalent geometry : bond 0.00397 (12646) covalent geometry : angle 0.63973 (17152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10209.96 seconds wall clock time: 177 minutes 46.92 seconds (10666.92 seconds total)