Starting phenix.real_space_refine on Tue Apr 29 13:01:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jio_36322/04_2025/8jio_36322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jio_36322/04_2025/8jio_36322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jio_36322/04_2025/8jio_36322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jio_36322/04_2025/8jio_36322.map" model { file = "/net/cci-nas-00/data/ceres_data/8jio_36322/04_2025/8jio_36322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jio_36322/04_2025/8jio_36322.cif" } resolution = 3.3 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= 0.002 sd= 0.031 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 34 5.16 5 C 5524 2.51 5 N 1452 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8698 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5350 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 35, 'TRANS': 641} Chain: "B" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1713 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 14, 'TRANS': 214} Time building chain proxies: 5.08, per 1000 atoms: 0.58 Number of scatterers: 8698 At special positions: 0 Unit cell: (117.432, 91.336, 152.848, 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 34 16.00 O 1688 8.00 N 1452 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 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: 1.96 Conformation dependent library (CDL) restraints added in 980.9 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 23 sheets defined 4.3% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.839A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.540A pdb=" N ASN A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.862A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.789A pdb=" N LYS B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.732A pdb=" N GLU B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.520A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.661A pdb=" N LEU A 277 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 51 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG A 273 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 271 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 71 removed outlier: 4.096A pdb=" N HIS A 70 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 78 " --> pdb=" O HIS A 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.811A pdb=" N SER A 117 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 106 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 239 " --> pdb=" O TRP A 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 191 removed outlier: 3.940A pdb=" N LYS A 187 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 189 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 202 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.693A pdb=" N VAL A 597 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ASN A 641 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.623A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 435 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.169A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 659 removed outlier: 4.537A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AB4, first strand: chain 'B' and resid 19 through 23 removed outlier: 3.513A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.751A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB7, first strand: chain 'B' and resid 130 through 139 removed outlier: 3.526A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 132 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 176 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.701A pdb=" N LYS B 145 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 197 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.533A pdb=" N GLN C 5 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS C 22 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 78 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.676A pdb=" N ALA C 91 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 98 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 51 Processing sheet with id=AC3, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.629A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C 149 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER C 189 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 190 " --> pdb=" O HIS C 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.629A pdb=" N GLY C 148 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS C 152 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU C 187 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 154 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 178 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 162 through 163 141 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2770 1.34 - 1.46: 2142 1.46 - 1.58: 3969 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 8920 Sorted by residual: bond pdb=" N ILE A 584 " pdb=" CA ILE A 584 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.58e+00 bond pdb=" N LEU A 582 " pdb=" CA LEU A 582 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.31e-02 5.83e+03 6.39e+00 bond pdb=" N GLU A 583 " pdb=" CA GLU A 583 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.20e-02 6.94e+03 4.73e+00 bond pdb=" N THR A 581 " pdb=" CA THR A 581 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.27e-02 6.20e+03 4.60e+00 bond pdb=" C TYR A 39 " pdb=" N PRO A 40 " ideal model delta sigma weight residual 1.326 1.353 -0.027 1.44e-02 4.82e+03 3.53e+00 ... (remaining 8915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11879 1.48 - 2.96: 224 2.96 - 4.44: 35 4.44 - 5.92: 9 5.92 - 7.40: 2 Bond angle restraints: 12149 Sorted by residual: angle pdb=" N TYR A 351 " pdb=" CA TYR A 351 " pdb=" C TYR A 351 " ideal model delta sigma weight residual 114.75 107.35 7.40 1.26e+00 6.30e-01 3.45e+01 angle pdb=" N VAL A 503 " pdb=" CA VAL A 503 " pdb=" C VAL A 503 " ideal model delta sigma weight residual 113.47 109.28 4.19 1.01e+00 9.80e-01 1.72e+01 angle pdb=" C LEU A 582 " pdb=" CA LEU A 582 " pdb=" CB LEU A 582 " ideal model delta sigma weight residual 109.84 116.04 -6.20 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N ALA A 352 " ideal model delta sigma weight residual 119.80 115.46 4.34 1.34e+00 5.57e-01 1.05e+01 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 106.21 109.52 -3.31 1.07e+00 8.73e-01 9.57e+00 ... (remaining 12144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.09: 5019 14.09 - 28.19: 198 28.19 - 42.28: 52 42.28 - 56.38: 11 56.38 - 70.47: 6 Dihedral angle restraints: 5286 sinusoidal: 2026 harmonic: 3260 Sorted by residual: dihedral pdb=" CA VAL A 350 " pdb=" C VAL A 350 " pdb=" N TYR A 351 " pdb=" CA TYR A 351 " ideal model delta harmonic sigma weight residual 180.00 157.87 22.13 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -115.75 29.75 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" C LEU A 582 " pdb=" N LEU A 582 " pdb=" CA LEU A 582 " pdb=" CB LEU A 582 " ideal model delta harmonic sigma weight residual -122.60 -130.40 7.80 0 2.50e+00 1.60e-01 9.75e+00 ... (remaining 5283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1206 0.075 - 0.151: 145 0.151 - 0.226: 3 0.226 - 0.302: 0 0.302 - 0.377: 1 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CG LEU A 582 " pdb=" CB LEU A 582 " pdb=" CD1 LEU A 582 " pdb=" CD2 LEU A 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 582 " pdb=" N LEU A 582 " pdb=" C LEU A 582 " pdb=" CB LEU A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1352 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 140 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO B 141 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.25e+00 pdb=" N PRO B 80 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 127 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO C 128 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 128 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 128 " 0.027 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 905 2.76 - 3.29: 8112 3.29 - 3.83: 13606 3.83 - 4.36: 15743 4.36 - 4.90: 26733 Nonbonded interactions: 65099 Sorted by model distance: nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLU A 340 " pdb=" OG SER B 56 " model vdw 2.259 3.040 nonbonded pdb=" O TYR B 49 " pdb=" OG1 THR B 53 " model vdw 2.270 3.040 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" NE2 GLN B 89 " model vdw 2.283 3.120 ... (remaining 65094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 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 : 0.002 0.037 8929 Z= 0.122 Angle : 0.520 7.403 12167 Z= 0.310 Chirality : 0.044 0.377 1355 Planarity : 0.004 0.062 1563 Dihedral : 8.535 70.474 3175 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.53 % Favored : 91.38 % Rotamer: Outliers : 3.78 % Allowed : 5.82 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.21), residues: 1114 helix: -4.23 (0.38), residues: 30 sheet: -2.90 (0.29), residues: 257 loop : -3.35 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 36 HIS 0.001 0.000 HIS A 625 PHE 0.005 0.001 PHE B 139 TYR 0.005 0.001 TYR C 53 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.32035 ( 138) hydrogen bonds : angle 11.55081 ( 336) SS BOND : bond 0.00086 ( 9) SS BOND : angle 0.41484 ( 18) covalent geometry : bond 0.00205 ( 8920) covalent geometry : angle 0.51995 (12149) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.1587 (OUTLIER) cc_final: 0.1300 (m) REVERT: A 55 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6348 (mt) REVERT: A 60 PHE cc_start: 0.6994 (m-80) cc_final: 0.6412 (m-80) REVERT: A 82 ASN cc_start: 0.6932 (m-40) cc_final: 0.6524 (m-40) REVERT: A 274 THR cc_start: 0.6818 (p) cc_final: 0.6563 (p) REVERT: A 298 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6657 (mt-10) REVERT: A 378 LYS cc_start: 0.7706 (pttm) cc_final: 0.7391 (pttm) REVERT: A 396 TYR cc_start: 0.8387 (m-80) cc_final: 0.7979 (m-10) REVERT: A 406 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7391 (mt-10) REVERT: A 422 ASN cc_start: 0.7320 (m-40) cc_final: 0.7115 (m110) REVERT: A 442 ASP cc_start: 0.6840 (m-30) cc_final: 0.6537 (m-30) REVERT: A 472 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6009 (pt) REVERT: A 547 THR cc_start: 0.7861 (m) cc_final: 0.7598 (p) REVERT: A 556 ASN cc_start: 0.7664 (m-40) cc_final: 0.7310 (m-40) REVERT: A 573 THR cc_start: 0.8783 (m) cc_final: 0.8521 (p) REVERT: A 578 ASP cc_start: 0.7042 (m-30) cc_final: 0.6599 (m-30) REVERT: A 581 THR cc_start: 0.8308 (p) cc_final: 0.7930 (p) REVERT: A 583 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6253 (mt-10) REVERT: A 584 ILE cc_start: 0.4816 (OUTLIER) cc_final: 0.4556 (pt) REVERT: A 612 TYR cc_start: 0.7081 (m-80) cc_final: 0.6253 (m-80) REVERT: A 624 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6481 (pt) REVERT: A 643 PHE cc_start: 0.5231 (m-80) cc_final: 0.4791 (m-80) REVERT: A 645 THR cc_start: 0.6690 (p) cc_final: 0.6006 (t) REVERT: B 107 LYS cc_start: 0.8417 (mtmp) cc_final: 0.8151 (ptpp) REVERT: B 108 ARG cc_start: 0.7005 (mmt90) cc_final: 0.6664 (mmt90) REVERT: B 123 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7922 (mt-10) REVERT: B 148 TRP cc_start: 0.5480 (OUTLIER) cc_final: 0.5203 (m100) REVERT: B 177 SER cc_start: 0.7074 (m) cc_final: 0.6568 (p) REVERT: B 179 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6025 (tm) REVERT: B 181 LEU cc_start: 0.8347 (mt) cc_final: 0.7802 (mt) REVERT: C 75 LYS cc_start: 0.8650 (ptmt) cc_final: 0.7850 (ptpp) REVERT: C 78 PHE cc_start: 0.7710 (p90) cc_final: 0.7452 (p90) REVERT: C 84 SER cc_start: 0.7689 (p) cc_final: 0.7172 (p) REVERT: C 92 VAL cc_start: 0.8236 (t) cc_final: 0.7682 (p) REVERT: C 179 LEU cc_start: 0.7936 (mt) cc_final: 0.7718 (mt) REVERT: C 220 VAL cc_start: 0.7528 (t) cc_final: 0.6972 (p) outliers start: 37 outliers final: 17 residues processed: 300 average time/residue: 0.2189 time to fit residues: 88.7191 Evaluate side-chains 253 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 228 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 149 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 62 ASN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 135 GLN A 185 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 641 ASN B 6 GLN B 27 GLN B 38 GLN B 89 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN C 58 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.195182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.162640 restraints weight = 15358.560| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.98 r_work: 0.3921 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 8929 Z= 0.270 Angle : 0.734 9.045 12167 Z= 0.374 Chirality : 0.050 0.191 1355 Planarity : 0.006 0.064 1563 Dihedral : 7.664 87.095 1262 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.22 % Favored : 88.60 % Rotamer: Outliers : 5.31 % Allowed : 12.56 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.08 (0.22), residues: 1114 helix: -3.77 (0.58), residues: 31 sheet: -2.27 (0.29), residues: 284 loop : -3.05 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 34 HIS 0.005 0.001 HIS A 339 PHE 0.021 0.003 PHE A 56 TYR 0.025 0.002 TYR A 313 ARG 0.014 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 138) hydrogen bonds : angle 8.00456 ( 336) SS BOND : bond 0.01137 ( 9) SS BOND : angle 1.44294 ( 18) covalent geometry : bond 0.00588 ( 8920) covalent geometry : angle 0.73219 (12149) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.7751 (mt0) cc_final: 0.7528 (mt0) REVERT: A 57 LEU cc_start: 0.7713 (mt) cc_final: 0.7419 (mm) REVERT: A 60 PHE cc_start: 0.7403 (m-80) cc_final: 0.6775 (m-80) REVERT: A 62 ASN cc_start: 0.7301 (m110) cc_final: 0.7033 (m-40) REVERT: A 202 LYS cc_start: 0.6110 (mttt) cc_final: 0.5261 (mtmt) REVERT: A 228 ASP cc_start: 0.7215 (m-30) cc_final: 0.6835 (m-30) REVERT: A 298 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 320 VAL cc_start: 0.7958 (m) cc_final: 0.7113 (p) REVERT: A 350 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7658 (p) REVERT: A 355 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7589 (ttt180) REVERT: A 392 PHE cc_start: 0.7636 (m-80) cc_final: 0.7200 (m-80) REVERT: A 396 TYR cc_start: 0.8543 (m-80) cc_final: 0.8178 (m-10) REVERT: A 422 ASN cc_start: 0.8103 (m-40) cc_final: 0.7866 (m110) REVERT: A 434 ILE cc_start: 0.8730 (mp) cc_final: 0.8475 (mt) REVERT: A 455 LEU cc_start: 0.8263 (tm) cc_final: 0.8025 (tt) REVERT: A 468 ILE cc_start: 0.8570 (mt) cc_final: 0.8342 (mt) REVERT: A 509 ARG cc_start: 0.7389 (mtt180) cc_final: 0.6955 (mmt90) REVERT: A 556 ASN cc_start: 0.8098 (m-40) cc_final: 0.7808 (m-40) REVERT: A 562 PHE cc_start: 0.7427 (m-10) cc_final: 0.7028 (m-80) REVERT: A 565 PHE cc_start: 0.7194 (t80) cc_final: 0.6911 (t80) REVERT: A 578 ASP cc_start: 0.8097 (m-30) cc_final: 0.7477 (m-30) REVERT: A 583 GLU cc_start: 0.7854 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 586 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: A 612 TYR cc_start: 0.7642 (m-80) cc_final: 0.6517 (m-80) REVERT: A 624 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6970 (pt) REVERT: A 627 ASP cc_start: 0.5586 (p0) cc_final: 0.5209 (p0) REVERT: A 643 PHE cc_start: 0.5935 (m-80) cc_final: 0.5448 (m-80) REVERT: B 24 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7559 (mtp85) REVERT: B 93 ASN cc_start: 0.7297 (p0) cc_final: 0.6970 (p0) REVERT: B 108 ARG cc_start: 0.7884 (mmt90) cc_final: 0.7524 (mmt90) REVERT: B 123 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 142 ARG cc_start: 0.8039 (ptp90) cc_final: 0.7609 (ptp90) REVERT: B 147 GLN cc_start: 0.7129 (tm-30) cc_final: 0.6717 (tm-30) REVERT: B 177 SER cc_start: 0.7975 (m) cc_final: 0.7640 (p) REVERT: C 57 THR cc_start: 0.8314 (p) cc_final: 0.7942 (t) REVERT: C 75 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8345 (ptpp) REVERT: C 78 PHE cc_start: 0.8455 (p90) cc_final: 0.8228 (p90) REVERT: C 92 VAL cc_start: 0.8517 (t) cc_final: 0.8213 (p) REVERT: C 109 MET cc_start: 0.8281 (mmt) cc_final: 0.7886 (mtm) REVERT: C 187 LEU cc_start: 0.8043 (pp) cc_final: 0.7575 (pt) REVERT: C 201 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 218 LYS cc_start: 0.8003 (mmmm) cc_final: 0.7728 (mmmm) outliers start: 52 outliers final: 29 residues processed: 300 average time/residue: 0.2088 time to fit residues: 84.8130 Evaluate side-chains 277 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 67 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 625 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.196295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.164328 restraints weight = 15484.869| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.96 r_work: 0.3950 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 8929 Z= 0.154 Angle : 0.674 19.197 12167 Z= 0.337 Chirality : 0.048 0.412 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.216 59.698 1244 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.31 % Rotamer: Outliers : 5.01 % Allowed : 17.16 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.79 (0.22), residues: 1114 helix: -3.55 (0.67), residues: 31 sheet: -2.05 (0.29), residues: 299 loop : -2.86 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 PHE 0.014 0.001 PHE A 56 TYR 0.016 0.001 TYR C 50 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 138) hydrogen bonds : angle 7.04370 ( 336) SS BOND : bond 0.00676 ( 9) SS BOND : angle 3.17571 ( 18) covalent geometry : bond 0.00374 ( 8920) covalent geometry : angle 0.66339 (12149) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7632 (mt) cc_final: 0.7064 (mm) REVERT: A 60 PHE cc_start: 0.7252 (m-80) cc_final: 0.6665 (m-80) REVERT: A 62 ASN cc_start: 0.7342 (m-40) cc_final: 0.6837 (m-40) REVERT: A 320 VAL cc_start: 0.7659 (m) cc_final: 0.7426 (m) REVERT: A 355 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7273 (ttt180) REVERT: A 396 TYR cc_start: 0.8502 (m-80) cc_final: 0.8019 (m-10) REVERT: A 422 ASN cc_start: 0.7995 (m-40) cc_final: 0.7686 (m110) REVERT: A 434 ILE cc_start: 0.8659 (mp) cc_final: 0.8388 (mt) REVERT: A 523 THR cc_start: 0.8209 (p) cc_final: 0.7893 (p) REVERT: A 556 ASN cc_start: 0.7989 (m-40) cc_final: 0.7746 (m-40) REVERT: A 565 PHE cc_start: 0.7107 (t80) cc_final: 0.6802 (t80) REVERT: A 576 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7194 (t) REVERT: A 583 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 586 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7263 (m-30) REVERT: A 612 TYR cc_start: 0.7657 (m-80) cc_final: 0.6554 (m-80) REVERT: A 624 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7139 (pt) REVERT: A 627 ASP cc_start: 0.5631 (p0) cc_final: 0.5248 (p0) REVERT: A 643 PHE cc_start: 0.5825 (m-80) cc_final: 0.5353 (m-80) REVERT: B 74 THR cc_start: 0.8135 (m) cc_final: 0.7887 (t) REVERT: B 106 ILE cc_start: 0.8635 (mp) cc_final: 0.8412 (mp) REVERT: B 108 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7459 (mmt90) REVERT: B 123 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 142 ARG cc_start: 0.7989 (ptp90) cc_final: 0.7591 (ptp90) REVERT: B 147 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6484 (tm-30) REVERT: B 185 ASP cc_start: 0.7694 (m-30) cc_final: 0.7473 (m-30) REVERT: C 75 LYS cc_start: 0.8779 (ptmt) cc_final: 0.8420 (ptmt) REVERT: C 77 GLN cc_start: 0.8323 (pt0) cc_final: 0.8100 (pt0) REVERT: C 92 VAL cc_start: 0.8594 (t) cc_final: 0.8267 (p) REVERT: C 109 MET cc_start: 0.8242 (mmt) cc_final: 0.7817 (mtm) REVERT: C 187 LEU cc_start: 0.7925 (pp) cc_final: 0.7509 (pt) REVERT: C 218 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7766 (mmmm) outliers start: 49 outliers final: 32 residues processed: 273 average time/residue: 0.2425 time to fit residues: 89.8778 Evaluate side-chains 258 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.1980 chunk 103 optimal weight: 0.9980 chunk 50 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.196821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165025 restraints weight = 15406.285| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.96 r_work: 0.3958 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8929 Z= 0.136 Angle : 0.628 11.714 12167 Z= 0.317 Chirality : 0.047 0.286 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.962 56.981 1242 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.86 % Favored : 89.05 % Rotamer: Outliers : 4.70 % Allowed : 17.98 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.52 (0.23), residues: 1114 helix: -3.48 (0.69), residues: 31 sheet: -1.84 (0.29), residues: 298 loop : -2.67 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 34 HIS 0.003 0.000 HIS A 245 PHE 0.018 0.001 PHE A 497 TYR 0.017 0.001 TYR C 50 ARG 0.006 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 138) hydrogen bonds : angle 6.60216 ( 336) SS BOND : bond 0.00496 ( 9) SS BOND : angle 2.42152 ( 18) covalent geometry : bond 0.00330 ( 8920) covalent geometry : angle 0.62155 (12149) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7273 (mm) REVERT: A 60 PHE cc_start: 0.7199 (m-80) cc_final: 0.6697 (m-80) REVERT: A 62 ASN cc_start: 0.7366 (m-40) cc_final: 0.6828 (m-40) REVERT: A 98 LYS cc_start: 0.7235 (mtmm) cc_final: 0.6930 (mppt) REVERT: A 310 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7604 (tttp) REVERT: A 349 SER cc_start: 0.8709 (m) cc_final: 0.8172 (p) REVERT: A 355 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7253 (ttt180) REVERT: A 396 TYR cc_start: 0.8483 (m-80) cc_final: 0.7990 (m-10) REVERT: A 523 THR cc_start: 0.8171 (p) cc_final: 0.7858 (p) REVERT: A 556 ASN cc_start: 0.7948 (m-40) cc_final: 0.7702 (m-40) REVERT: A 565 PHE cc_start: 0.7043 (t80) cc_final: 0.6703 (t80) REVERT: A 583 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 612 TYR cc_start: 0.7665 (m-80) cc_final: 0.6552 (m-80) REVERT: A 624 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7164 (pt) REVERT: A 627 ASP cc_start: 0.5683 (p0) cc_final: 0.5425 (p0) REVERT: A 643 PHE cc_start: 0.5808 (m-80) cc_final: 0.5338 (m-80) REVERT: A 656 VAL cc_start: 0.7199 (t) cc_final: 0.6938 (p) REVERT: B 74 THR cc_start: 0.8162 (m) cc_final: 0.7901 (t) REVERT: B 108 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7522 (mmt90) REVERT: B 123 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8192 (mt-10) REVERT: B 142 ARG cc_start: 0.7972 (ptp90) cc_final: 0.7603 (ptp90) REVERT: B 147 GLN cc_start: 0.7010 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 164 THR cc_start: 0.7824 (t) cc_final: 0.7027 (m) REVERT: C 109 MET cc_start: 0.8242 (mmt) cc_final: 0.7876 (mtm) outliers start: 46 outliers final: 38 residues processed: 255 average time/residue: 0.2320 time to fit residues: 78.9021 Evaluate side-chains 262 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** 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 = 0.4475 r_free = 0.4475 target = 0.195025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163011 restraints weight = 15417.078| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.89 r_work: 0.3948 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8929 Z= 0.138 Angle : 0.650 14.289 12167 Z= 0.324 Chirality : 0.047 0.327 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.045 56.127 1242 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.23 % Favored : 89.68 % Rotamer: Outliers : 5.21 % Allowed : 18.08 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.36 (0.23), residues: 1114 helix: -3.68 (0.62), residues: 31 sheet: -1.74 (0.30), residues: 296 loop : -2.54 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 34 HIS 0.004 0.001 HIS A 245 PHE 0.015 0.001 PHE A 497 TYR 0.019 0.001 TYR C 50 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 138) hydrogen bonds : angle 6.42655 ( 336) SS BOND : bond 0.00978 ( 9) SS BOND : angle 3.30415 ( 18) covalent geometry : bond 0.00319 ( 8920) covalent geometry : angle 0.63842 (12149) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 60 PHE cc_start: 0.7200 (m-80) cc_final: 0.6712 (m-80) REVERT: A 89 ASP cc_start: 0.3406 (OUTLIER) cc_final: 0.3021 (m-30) REVERT: A 98 LYS cc_start: 0.7182 (mtmm) cc_final: 0.6833 (mppt) REVERT: A 355 ARG cc_start: 0.7697 (ttt180) cc_final: 0.7211 (ttt180) REVERT: A 396 TYR cc_start: 0.8510 (m-80) cc_final: 0.7771 (m-10) REVERT: A 516 GLU cc_start: 0.7798 (tt0) cc_final: 0.7419 (tt0) REVERT: A 523 THR cc_start: 0.8133 (p) cc_final: 0.7818 (p) REVERT: A 556 ASN cc_start: 0.7828 (m-40) cc_final: 0.7622 (m-40) REVERT: A 565 PHE cc_start: 0.7055 (t80) cc_final: 0.6798 (t80) REVERT: A 583 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7471 (mt-10) REVERT: A 612 TYR cc_start: 0.7680 (m-80) cc_final: 0.6597 (m-80) REVERT: A 627 ASP cc_start: 0.5293 (p0) cc_final: 0.5007 (p0) REVERT: A 629 LEU cc_start: 0.7816 (mm) cc_final: 0.7368 (mt) REVERT: A 643 PHE cc_start: 0.5840 (m-80) cc_final: 0.5461 (m-80) REVERT: A 656 VAL cc_start: 0.7204 (t) cc_final: 0.6911 (p) REVERT: B 108 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7534 (mmt90) REVERT: B 123 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 142 ARG cc_start: 0.7948 (ptp90) cc_final: 0.7561 (ptp90) REVERT: B 147 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6776 (tm-30) REVERT: C 57 THR cc_start: 0.8330 (p) cc_final: 0.8017 (t) REVERT: C 75 LYS cc_start: 0.8790 (ptmt) cc_final: 0.8242 (ptpp) REVERT: C 77 GLN cc_start: 0.8453 (pt0) cc_final: 0.8216 (pt0) REVERT: C 109 MET cc_start: 0.8232 (mmt) cc_final: 0.7901 (mtm) outliers start: 51 outliers final: 36 residues processed: 262 average time/residue: 0.2343 time to fit residues: 81.9264 Evaluate side-chains 259 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** 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 = 0.4431 r_free = 0.4431 target = 0.191182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.158830 restraints weight = 15243.813| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.91 r_work: 0.3894 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8929 Z= 0.194 Angle : 0.706 15.306 12167 Z= 0.353 Chirality : 0.049 0.332 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.230 56.012 1241 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.58 % Favored : 88.24 % Rotamer: Outliers : 4.39 % Allowed : 18.90 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.39 (0.23), residues: 1114 helix: -3.68 (0.61), residues: 36 sheet: -1.71 (0.29), residues: 296 loop : -2.57 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 34 HIS 0.005 0.001 HIS A 245 PHE 0.019 0.002 PHE A 497 TYR 0.018 0.001 TYR C 50 ARG 0.006 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 138) hydrogen bonds : angle 6.52223 ( 336) SS BOND : bond 0.00320 ( 9) SS BOND : angle 3.40078 ( 18) covalent geometry : bond 0.00434 ( 8920) covalent geometry : angle 0.69467 (12149) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 249 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7354 (mm) REVERT: A 60 PHE cc_start: 0.7167 (m-80) cc_final: 0.6714 (m-80) REVERT: A 89 ASP cc_start: 0.3755 (OUTLIER) cc_final: 0.3303 (m-30) REVERT: A 98 LYS cc_start: 0.7348 (mtmm) cc_final: 0.6949 (mppt) REVERT: A 265 TYR cc_start: 0.5773 (m-80) cc_final: 0.5035 (m-80) REVERT: A 355 ARG cc_start: 0.7759 (ttt180) cc_final: 0.7340 (ttt180) REVERT: A 392 PHE cc_start: 0.7631 (m-80) cc_final: 0.7280 (m-80) REVERT: A 396 TYR cc_start: 0.8498 (m-80) cc_final: 0.7758 (m-10) REVERT: A 516 GLU cc_start: 0.7849 (tt0) cc_final: 0.7414 (tt0) REVERT: A 523 THR cc_start: 0.8220 (p) cc_final: 0.7909 (p) REVERT: A 556 ASN cc_start: 0.7891 (m-40) cc_final: 0.7674 (m-40) REVERT: A 583 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 612 TYR cc_start: 0.7814 (m-80) cc_final: 0.6731 (m-80) REVERT: A 627 ASP cc_start: 0.5614 (p0) cc_final: 0.5215 (p0) REVERT: A 629 LEU cc_start: 0.7867 (mm) cc_final: 0.7437 (mt) REVERT: A 654 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6785 (mm-30) REVERT: A 656 VAL cc_start: 0.7223 (t) cc_final: 0.6905 (p) REVERT: B 67 SER cc_start: 0.8379 (t) cc_final: 0.8148 (p) REVERT: B 107 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8609 (ptpp) REVERT: B 108 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7611 (mmt90) REVERT: B 123 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8112 (mt-10) REVERT: B 142 ARG cc_start: 0.7939 (ptp90) cc_final: 0.7579 (ptp90) REVERT: B 147 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6674 (tm-30) REVERT: B 181 LEU cc_start: 0.8441 (mt) cc_final: 0.8144 (tp) REVERT: C 35 THR cc_start: 0.7841 (p) cc_final: 0.7469 (p) REVERT: C 57 THR cc_start: 0.8452 (p) cc_final: 0.8160 (t) REVERT: C 68 THR cc_start: 0.8750 (p) cc_final: 0.8529 (t) REVERT: C 75 LYS cc_start: 0.8850 (ptmt) cc_final: 0.8507 (ptpp) REVERT: C 109 MET cc_start: 0.8253 (mmt) cc_final: 0.7895 (mtm) outliers start: 43 outliers final: 34 residues processed: 270 average time/residue: 0.2327 time to fit residues: 84.1965 Evaluate side-chains 275 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.1980 chunk 96 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** 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 = 0.4470 r_free = 0.4470 target = 0.194421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162190 restraints weight = 15488.740| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.96 r_work: 0.3937 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8929 Z= 0.120 Angle : 0.674 17.674 12167 Z= 0.334 Chirality : 0.047 0.328 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.021 55.495 1241 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.69 % Favored : 90.22 % Rotamer: Outliers : 5.11 % Allowed : 19.31 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.20 (0.23), residues: 1114 helix: -3.90 (0.63), residues: 30 sheet: -1.58 (0.28), residues: 306 loop : -2.44 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 34 HIS 0.003 0.001 HIS A 245 PHE 0.028 0.001 PHE A 565 TYR 0.016 0.001 TYR A 365 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 138) hydrogen bonds : angle 6.19658 ( 336) SS BOND : bond 0.00664 ( 9) SS BOND : angle 3.42257 ( 18) covalent geometry : bond 0.00277 ( 8920) covalent geometry : angle 0.66170 (12149) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7075 (mm) REVERT: A 60 PHE cc_start: 0.7122 (m-80) cc_final: 0.6715 (m-80) REVERT: A 89 ASP cc_start: 0.3512 (OUTLIER) cc_final: 0.3086 (m-30) REVERT: A 98 LYS cc_start: 0.7240 (mtmm) cc_final: 0.6833 (mppt) REVERT: A 273 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7181 (mtt180) REVERT: A 355 ARG cc_start: 0.7710 (ttt180) cc_final: 0.7181 (ttt180) REVERT: A 378 LYS cc_start: 0.7595 (pttm) cc_final: 0.7392 (pttm) REVERT: A 396 TYR cc_start: 0.8473 (m-80) cc_final: 0.7945 (m-10) REVERT: A 455 LEU cc_start: 0.8175 (tp) cc_final: 0.7886 (pp) REVERT: A 509 ARG cc_start: 0.7450 (mtt180) cc_final: 0.7152 (mmt90) REVERT: A 523 THR cc_start: 0.8147 (p) cc_final: 0.7835 (p) REVERT: A 529 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7712 (mmmm) REVERT: A 556 ASN cc_start: 0.7855 (m-40) cc_final: 0.7632 (m-40) REVERT: A 565 PHE cc_start: 0.7119 (t80) cc_final: 0.6851 (t80) REVERT: A 583 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 586 ASP cc_start: 0.7431 (p0) cc_final: 0.7117 (p0) REVERT: A 612 TYR cc_start: 0.7772 (m-80) cc_final: 0.6681 (m-80) REVERT: A 627 ASP cc_start: 0.5346 (p0) cc_final: 0.5011 (p0) REVERT: A 629 LEU cc_start: 0.7787 (mm) cc_final: 0.7350 (mt) REVERT: A 656 VAL cc_start: 0.7232 (t) cc_final: 0.6924 (p) REVERT: B 9 SER cc_start: 0.8113 (m) cc_final: 0.7829 (p) REVERT: B 107 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (ptpp) REVERT: B 108 ARG cc_start: 0.7874 (mmt90) cc_final: 0.7537 (mmt90) REVERT: B 123 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8209 (mt-10) REVERT: B 142 ARG cc_start: 0.7934 (ptp90) cc_final: 0.7585 (ptp90) REVERT: B 147 GLN cc_start: 0.7119 (tm-30) cc_final: 0.6696 (tm-30) REVERT: C 35 THR cc_start: 0.7865 (p) cc_final: 0.7428 (p) REVERT: C 43 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8309 (mtmt) REVERT: C 57 THR cc_start: 0.8400 (p) cc_final: 0.8126 (t) REVERT: C 68 THR cc_start: 0.8775 (p) cc_final: 0.8530 (t) REVERT: C 75 LYS cc_start: 0.8760 (ptmt) cc_final: 0.8478 (ptpp) REVERT: C 109 MET cc_start: 0.8260 (mmt) cc_final: 0.7945 (mtm) outliers start: 50 outliers final: 39 residues processed: 264 average time/residue: 0.2334 time to fit residues: 81.5584 Evaluate side-chains 276 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.193212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.160734 restraints weight = 15588.099| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 4.00 r_work: 0.3921 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8929 Z= 0.135 Angle : 0.685 15.314 12167 Z= 0.339 Chirality : 0.048 0.289 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.040 55.485 1241 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.13 % Favored : 88.69 % Rotamer: Outliers : 4.39 % Allowed : 20.33 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.07 (0.23), residues: 1114 helix: -3.34 (0.77), residues: 24 sheet: -1.55 (0.28), residues: 304 loop : -2.36 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 34 HIS 0.002 0.000 HIS A 245 PHE 0.020 0.001 PHE A 565 TYR 0.016 0.001 TYR A 365 ARG 0.006 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 138) hydrogen bonds : angle 6.20912 ( 336) SS BOND : bond 0.00495 ( 9) SS BOND : angle 3.39715 ( 18) covalent geometry : bond 0.00312 ( 8920) covalent geometry : angle 0.67320 (12149) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7130 (mm) REVERT: A 60 PHE cc_start: 0.7172 (m-80) cc_final: 0.6737 (m-80) REVERT: A 62 ASN cc_start: 0.7636 (m-40) cc_final: 0.7027 (m-40) REVERT: A 98 LYS cc_start: 0.7463 (mtmm) cc_final: 0.7033 (mppt) REVERT: A 273 ARG cc_start: 0.7376 (mtt180) cc_final: 0.7147 (mtt180) REVERT: A 355 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7415 (ttt180) REVERT: A 392 PHE cc_start: 0.7568 (m-80) cc_final: 0.7125 (m-80) REVERT: A 455 LEU cc_start: 0.8225 (tp) cc_final: 0.7873 (pp) REVERT: A 509 ARG cc_start: 0.7471 (mtt180) cc_final: 0.7168 (mmt90) REVERT: A 516 GLU cc_start: 0.7760 (tt0) cc_final: 0.7284 (tt0) REVERT: A 523 THR cc_start: 0.8061 (p) cc_final: 0.7765 (p) REVERT: A 529 LYS cc_start: 0.8263 (mmmm) cc_final: 0.7740 (mmmm) REVERT: A 565 PHE cc_start: 0.7094 (t80) cc_final: 0.6821 (t80) REVERT: A 577 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7746 (ttt90) REVERT: A 583 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 586 ASP cc_start: 0.7523 (p0) cc_final: 0.7226 (p0) REVERT: A 612 TYR cc_start: 0.7761 (m-80) cc_final: 0.6691 (m-80) REVERT: A 627 ASP cc_start: 0.5502 (p0) cc_final: 0.5154 (p0) REVERT: A 629 LEU cc_start: 0.7807 (mm) cc_final: 0.7398 (mt) REVERT: A 656 VAL cc_start: 0.7243 (t) cc_final: 0.6905 (p) REVERT: B 9 SER cc_start: 0.8156 (m) cc_final: 0.7835 (p) REVERT: B 107 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8554 (ptpp) REVERT: B 108 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7573 (mmt90) REVERT: B 123 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8230 (mt-10) REVERT: B 142 ARG cc_start: 0.7948 (ptp90) cc_final: 0.7591 (ptp90) REVERT: B 147 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6603 (tm-30) REVERT: B 181 LEU cc_start: 0.8382 (mt) cc_final: 0.8048 (tp) REVERT: C 35 THR cc_start: 0.8040 (p) cc_final: 0.7688 (p) REVERT: C 43 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8324 (mtmt) REVERT: C 57 THR cc_start: 0.8395 (p) cc_final: 0.8118 (t) REVERT: C 68 THR cc_start: 0.8823 (p) cc_final: 0.8572 (t) REVERT: C 75 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8426 (ptpp) REVERT: C 109 MET cc_start: 0.8265 (mmt) cc_final: 0.7938 (mtm) outliers start: 43 outliers final: 35 residues processed: 266 average time/residue: 0.3024 time to fit residues: 108.1999 Evaluate side-chains 277 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 40.0000 chunk 72 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.192067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159559 restraints weight = 15332.630| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 3.96 r_work: 0.3898 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8929 Z= 0.166 Angle : 0.721 17.865 12167 Z= 0.358 Chirality : 0.049 0.348 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.104 55.604 1239 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.31 % Favored : 88.51 % Rotamer: Outliers : 3.88 % Allowed : 20.22 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.09 (0.23), residues: 1114 helix: -3.56 (0.64), residues: 30 sheet: -1.51 (0.28), residues: 309 loop : -2.37 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 34 HIS 0.002 0.001 HIS B 198 PHE 0.017 0.001 PHE A 194 TYR 0.016 0.001 TYR A 365 ARG 0.005 0.001 ARG C 66 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 138) hydrogen bonds : angle 6.24319 ( 336) SS BOND : bond 0.00722 ( 9) SS BOND : angle 3.56230 ( 18) covalent geometry : bond 0.00374 ( 8920) covalent geometry : angle 0.70859 (12149) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7254 (mm) REVERT: A 60 PHE cc_start: 0.7193 (m-80) cc_final: 0.6724 (m-80) REVERT: A 62 ASN cc_start: 0.7646 (m-40) cc_final: 0.7141 (m-40) REVERT: A 98 LYS cc_start: 0.7420 (mtmm) cc_final: 0.6960 (mppt) REVERT: A 320 VAL cc_start: 0.7753 (m) cc_final: 0.6970 (p) REVERT: A 355 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7278 (ttt180) REVERT: A 364 ASP cc_start: 0.7306 (t70) cc_final: 0.6962 (t0) REVERT: A 378 LYS cc_start: 0.7601 (pttm) cc_final: 0.7322 (pttm) REVERT: A 392 PHE cc_start: 0.7615 (m-80) cc_final: 0.7271 (m-80) REVERT: A 396 TYR cc_start: 0.8479 (m-80) cc_final: 0.7635 (m-10) REVERT: A 455 LEU cc_start: 0.8265 (tp) cc_final: 0.7995 (tt) REVERT: A 466 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7942 (ptm160) REVERT: A 509 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7133 (mmt90) REVERT: A 516 GLU cc_start: 0.7650 (tt0) cc_final: 0.7311 (tt0) REVERT: A 523 THR cc_start: 0.8084 (p) cc_final: 0.7724 (p) REVERT: A 529 LYS cc_start: 0.8338 (mmmm) cc_final: 0.7796 (mmmm) REVERT: A 565 PHE cc_start: 0.7172 (t80) cc_final: 0.6916 (t80) REVERT: A 577 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7742 (ttt90) REVERT: A 583 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 586 ASP cc_start: 0.7515 (p0) cc_final: 0.7207 (p0) REVERT: A 612 TYR cc_start: 0.7822 (m-80) cc_final: 0.6749 (m-80) REVERT: A 627 ASP cc_start: 0.5693 (p0) cc_final: 0.5267 (p0) REVERT: A 629 LEU cc_start: 0.7780 (mm) cc_final: 0.7366 (mt) REVERT: A 656 VAL cc_start: 0.7197 (t) cc_final: 0.6857 (p) REVERT: B 9 SER cc_start: 0.8163 (m) cc_final: 0.7840 (p) REVERT: B 107 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8562 (ptpp) REVERT: B 108 ARG cc_start: 0.7926 (mmt90) cc_final: 0.7589 (mmt90) REVERT: B 123 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8257 (mt-10) REVERT: B 142 ARG cc_start: 0.7948 (ptp90) cc_final: 0.7561 (ptp90) REVERT: B 147 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6625 (tm-30) REVERT: B 181 LEU cc_start: 0.8434 (mt) cc_final: 0.8083 (tp) REVERT: C 35 THR cc_start: 0.8250 (p) cc_final: 0.7989 (p) REVERT: C 43 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8350 (mtmt) REVERT: C 57 THR cc_start: 0.8446 (p) cc_final: 0.8164 (t) REVERT: C 68 THR cc_start: 0.8872 (p) cc_final: 0.8609 (t) REVERT: C 75 LYS cc_start: 0.8829 (ptmt) cc_final: 0.8520 (ptpp) REVERT: C 109 MET cc_start: 0.8265 (mmt) cc_final: 0.7951 (mtm) outliers start: 38 outliers final: 34 residues processed: 260 average time/residue: 0.2372 time to fit residues: 81.6166 Evaluate side-chains 271 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.191630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158575 restraints weight = 15491.076| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 4.05 r_work: 0.3896 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8929 Z= 0.154 Angle : 0.714 15.966 12167 Z= 0.355 Chirality : 0.048 0.309 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.142 56.110 1239 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.86 % Favored : 88.96 % Rotamer: Outliers : 3.88 % Allowed : 20.33 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.06 (0.24), residues: 1114 helix: -3.86 (0.61), residues: 30 sheet: -1.46 (0.28), residues: 320 loop : -2.36 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 34 HIS 0.003 0.001 HIS A 245 PHE 0.015 0.001 PHE A 565 TYR 0.016 0.001 TYR A 365 ARG 0.008 0.001 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 138) hydrogen bonds : angle 6.21743 ( 336) SS BOND : bond 0.00663 ( 9) SS BOND : angle 3.51203 ( 18) covalent geometry : bond 0.00350 ( 8920) covalent geometry : angle 0.70202 (12149) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.6975 (mm) REVERT: A 60 PHE cc_start: 0.7279 (m-80) cc_final: 0.6785 (m-80) REVERT: A 98 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7197 (mppt) REVERT: A 271 GLN cc_start: 0.7320 (mt0) cc_final: 0.7058 (mm-40) REVERT: A 273 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6798 (ptp90) REVERT: A 275 PHE cc_start: 0.7166 (m-10) cc_final: 0.6912 (m-10) REVERT: A 320 VAL cc_start: 0.7723 (m) cc_final: 0.7010 (p) REVERT: A 349 SER cc_start: 0.8719 (m) cc_final: 0.8202 (t) REVERT: A 364 ASP cc_start: 0.7286 (t70) cc_final: 0.6969 (t0) REVERT: A 378 LYS cc_start: 0.7654 (pttm) cc_final: 0.7343 (pttm) REVERT: A 392 PHE cc_start: 0.7614 (m-80) cc_final: 0.7251 (m-80) REVERT: A 466 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7833 (ptm160) REVERT: A 509 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7128 (mmt90) REVERT: A 516 GLU cc_start: 0.7618 (tt0) cc_final: 0.7305 (tt0) REVERT: A 523 THR cc_start: 0.8001 (p) cc_final: 0.7782 (p) REVERT: A 529 LYS cc_start: 0.8369 (mmmm) cc_final: 0.7833 (mmmm) REVERT: A 565 PHE cc_start: 0.7209 (t80) cc_final: 0.6983 (t80) REVERT: A 583 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 586 ASP cc_start: 0.7521 (p0) cc_final: 0.7231 (p0) REVERT: A 612 TYR cc_start: 0.7827 (m-80) cc_final: 0.6741 (m-80) REVERT: A 627 ASP cc_start: 0.5717 (p0) cc_final: 0.5328 (p0) REVERT: A 629 LEU cc_start: 0.7843 (mm) cc_final: 0.7448 (mt) REVERT: A 656 VAL cc_start: 0.7209 (t) cc_final: 0.6876 (p) REVERT: B 9 SER cc_start: 0.8136 (m) cc_final: 0.7796 (p) REVERT: B 107 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8560 (ptpp) REVERT: B 108 ARG cc_start: 0.7906 (mmt90) cc_final: 0.7553 (mmt90) REVERT: B 123 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8248 (mt-10) REVERT: B 142 ARG cc_start: 0.7949 (ptp90) cc_final: 0.7556 (ptp90) REVERT: B 147 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6609 (tm-30) REVERT: B 181 LEU cc_start: 0.8467 (mt) cc_final: 0.8121 (tp) REVERT: C 35 THR cc_start: 0.8326 (p) cc_final: 0.8117 (p) REVERT: C 43 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8310 (mtmt) REVERT: C 57 THR cc_start: 0.8468 (p) cc_final: 0.8183 (t) REVERT: C 68 THR cc_start: 0.8884 (p) cc_final: 0.8614 (t) REVERT: C 75 LYS cc_start: 0.8869 (ptmt) cc_final: 0.8561 (ptpp) REVERT: C 109 MET cc_start: 0.8262 (mmt) cc_final: 0.7925 (mtm) outliers start: 38 outliers final: 35 residues processed: 259 average time/residue: 0.2381 time to fit residues: 81.5513 Evaluate side-chains 275 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 543 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.3980 chunk 68 optimal weight: 0.0000 chunk 60 optimal weight: 0.0370 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.195760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163494 restraints weight = 15544.609| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 4.04 r_work: 0.3964 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8929 Z= 0.115 Angle : 0.691 17.963 12167 Z= 0.342 Chirality : 0.047 0.313 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.948 55.959 1239 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.78 % Favored : 90.13 % Rotamer: Outliers : 3.68 % Allowed : 21.04 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.91 (0.24), residues: 1114 helix: -3.71 (0.74), residues: 24 sheet: -1.37 (0.27), residues: 333 loop : -2.27 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 34 HIS 0.003 0.000 HIS A 245 PHE 0.015 0.001 PHE A 565 TYR 0.015 0.001 TYR A 365 ARG 0.011 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 138) hydrogen bonds : angle 5.94859 ( 336) SS BOND : bond 0.00573 ( 9) SS BOND : angle 3.49588 ( 18) covalent geometry : bond 0.00269 ( 8920) covalent geometry : angle 0.67784 (12149) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.86 seconds wall clock time: 88 minutes 39.75 seconds (5319.75 seconds total)