Starting phenix.real_space_refine on Thu Mar 13 06:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jio_36322/03_2025/8jio_36322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jio_36322/03_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_36322/03_2025/8jio_36322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jio_36322/03_2025/8jio_36322.map" model { file = "/net/cci-nas-00/data/ceres_data/8jio_36322/03_2025/8jio_36322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jio_36322/03_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.81, per 1000 atoms: 0.67 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: 2.57 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.07 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: 2.35 Time building geometry restraints manager: 2.57 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- 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 8920 Z= 0.138 Angle : 0.520 7.403 12149 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 *********************** 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 : 0.849 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: 0.2195 time to fit residues: 87.8976 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 : 0.959 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 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: 1.2384 ------------------------------------------------------------------------------- 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 625 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN C 58 ASN C 60 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 = 0.4510 r_free = 0.4510 target = 0.198826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167084 restraints weight = 15460.624| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.98 r_work: 0.3981 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8920 Z= 0.284 Angle : 0.656 9.340 12149 Z= 0.331 Chirality : 0.047 0.193 1355 Planarity : 0.006 0.061 1563 Dihedral : 7.233 79.478 1262 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.59 % Favored : 89.32 % Rotamer: Outliers : 4.70 % Allowed : 13.07 % Favored : 82.23 % 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: -3.98 (0.48), residues: 31 sheet: -2.37 (0.27), residues: 312 loop : -2.99 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 34 HIS 0.004 0.001 HIS A 339 PHE 0.019 0.002 PHE A 275 TYR 0.020 0.002 TYR A 313 ARG 0.011 0.001 ARG A 273 *********************** 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 309 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.3199 (OUTLIER) cc_final: 0.2994 (m) REVERT: A 60 PHE cc_start: 0.7342 (m-80) cc_final: 0.6733 (m-80) REVERT: A 82 ASN cc_start: 0.7046 (m-40) cc_final: 0.6823 (m-40) REVERT: A 202 LYS cc_start: 0.5978 (mttt) cc_final: 0.5138 (mtmm) REVERT: A 317 ASN cc_start: 0.6636 (m110) cc_final: 0.6349 (m110) REVERT: A 320 VAL cc_start: 0.7836 (m) cc_final: 0.7102 (p) REVERT: A 355 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7485 (ttt180) REVERT: A 360 ASN cc_start: 0.8148 (m-40) cc_final: 0.7912 (m-40) REVERT: A 382 VAL cc_start: 0.8457 (t) cc_final: 0.8091 (p) REVERT: A 392 PHE cc_start: 0.7489 (m-80) cc_final: 0.7100 (m-80) REVERT: A 396 TYR cc_start: 0.8512 (m-80) cc_final: 0.8114 (m-10) REVERT: A 402 ILE cc_start: 0.7548 (tp) cc_final: 0.7348 (tt) REVERT: A 434 ILE cc_start: 0.8677 (mp) cc_final: 0.8405 (mt) REVERT: A 487 ASN cc_start: 0.7853 (m-40) cc_final: 0.7563 (m-40) REVERT: A 509 ARG cc_start: 0.7337 (mtt180) cc_final: 0.6899 (mmt90) REVERT: A 547 THR cc_start: 0.8108 (m) cc_final: 0.7883 (p) REVERT: A 556 ASN cc_start: 0.8044 (m-40) cc_final: 0.7791 (m-40) REVERT: A 562 PHE cc_start: 0.7364 (m-10) cc_final: 0.7034 (m-80) REVERT: A 565 PHE cc_start: 0.7053 (t80) cc_final: 0.6793 (t80) REVERT: A 578 ASP cc_start: 0.8003 (m-30) cc_final: 0.7480 (m-30) REVERT: A 583 GLU cc_start: 0.7844 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 584 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5368 (pt) REVERT: A 586 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: A 612 TYR cc_start: 0.7420 (m-80) cc_final: 0.6363 (m-80) REVERT: A 624 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6790 (pt) REVERT: A 628 GLN cc_start: 0.6335 (mp10) cc_final: 0.5809 (mp10) REVERT: A 643 PHE cc_start: 0.5976 (m-80) cc_final: 0.5458 (m-80) REVERT: B 24 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.7434 (mtp85) REVERT: B 108 ARG cc_start: 0.7817 (mmt90) cc_final: 0.7450 (mmt90) REVERT: B 123 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 147 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6656 (tm-30) REVERT: B 177 SER cc_start: 0.7769 (m) cc_final: 0.7525 (p) REVERT: C 54 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8253 (t) REVERT: C 67 VAL cc_start: 0.8832 (p) cc_final: 0.8456 (m) REVERT: C 75 LYS cc_start: 0.8891 (ptmt) cc_final: 0.8225 (ptpp) REVERT: C 92 VAL cc_start: 0.8537 (t) cc_final: 0.8217 (p) REVERT: C 109 MET cc_start: 0.8288 (mmt) cc_final: 0.7874 (mtm) REVERT: C 187 LEU cc_start: 0.8010 (pp) cc_final: 0.7807 (pt) REVERT: C 201 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7431 (tm-30) outliers start: 46 outliers final: 24 residues processed: 283 average time/residue: 0.2133 time to fit residues: 81.2889 Evaluate side-chains 270 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 367 VAL 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 584 ILE 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 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 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 52 TYR Chi-restraints excluded: chain C residue 54 THR 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: 0.8980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** 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 = 0.4491 r_free = 0.4491 target = 0.196783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.164930 restraints weight = 15707.187| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 3.93 r_work: 0.3980 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8920 Z= 0.239 Angle : 0.629 9.556 12149 Z= 0.316 Chirality : 0.047 0.176 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.061 58.062 1245 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.43 % Favored : 90.48 % Rotamer: Outliers : 4.90 % Allowed : 16.24 % Favored : 78.86 % 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: -3.74 (0.22), residues: 1114 helix: -3.74 (0.59), residues: 31 sheet: -2.00 (0.29), residues: 288 loop : -2.82 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 34 HIS 0.004 0.001 HIS A 67 PHE 0.017 0.001 PHE A 562 TYR 0.016 0.001 TYR C 50 ARG 0.006 0.001 ARG A 273 *********************** 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 298 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6814 (mt) REVERT: A 60 PHE cc_start: 0.7214 (m-80) cc_final: 0.6664 (m-80) REVERT: A 82 ASN cc_start: 0.7107 (m-40) cc_final: 0.6905 (m-40) REVERT: A 202 LYS cc_start: 0.6123 (mttt) cc_final: 0.5219 (mtmt) REVERT: A 320 VAL cc_start: 0.7635 (m) cc_final: 0.7408 (m) REVERT: A 355 ARG cc_start: 0.7746 (ttt180) cc_final: 0.7334 (ttt180) REVERT: A 378 LYS cc_start: 0.7978 (pttm) cc_final: 0.7676 (pttm) REVERT: A 396 TYR cc_start: 0.8510 (m-80) cc_final: 0.8045 (m-10) REVERT: A 422 ASN cc_start: 0.7754 (m110) cc_final: 0.7434 (m110) REVERT: A 434 ILE cc_start: 0.8637 (mp) cc_final: 0.8376 (mt) REVERT: A 509 ARG cc_start: 0.7386 (mtt180) cc_final: 0.6948 (mmt90) REVERT: A 523 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7760 (p) REVERT: A 547 THR cc_start: 0.8051 (m) cc_final: 0.7836 (p) REVERT: A 556 ASN cc_start: 0.7966 (m-40) cc_final: 0.7722 (m-40) REVERT: A 565 PHE cc_start: 0.7059 (t80) cc_final: 0.6688 (t80) REVERT: A 583 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7363 (mt-10) REVERT: A 586 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: A 612 TYR cc_start: 0.7502 (m-80) cc_final: 0.6424 (m-80) REVERT: A 624 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6974 (pt) REVERT: A 627 ASP cc_start: 0.5732 (p0) cc_final: 0.5415 (p0) REVERT: A 643 PHE cc_start: 0.5876 (m-80) cc_final: 0.5371 (m-80) REVERT: B 24 ARG cc_start: 0.7871 (mtp-110) cc_final: 0.7477 (mtp85) REVERT: B 106 ILE cc_start: 0.8622 (mp) cc_final: 0.8379 (mp) REVERT: B 108 ARG cc_start: 0.7783 (mmt90) cc_final: 0.7419 (mmt90) REVERT: B 147 GLN cc_start: 0.6992 (tm-30) cc_final: 0.6469 (tm-30) REVERT: C 11 LEU cc_start: 0.7958 (mt) cc_final: 0.7724 (tp) REVERT: C 92 VAL cc_start: 0.8575 (t) cc_final: 0.8220 (p) REVERT: C 109 MET cc_start: 0.8106 (mmt) cc_final: 0.7792 (mtm) REVERT: C 187 LEU cc_start: 0.7922 (pp) cc_final: 0.7508 (pt) outliers start: 48 outliers final: 30 residues processed: 272 average time/residue: 0.2385 time to fit residues: 86.8740 Evaluate side-chains 267 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 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 244 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 367 VAL 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 560 LEU 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 142 ARG Chi-restraints excluded: chain B residue 194 CYS 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 119 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 58 ASN ** C 164 ASN ** 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 = 0.4484 r_free = 0.4484 target = 0.196414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.164708 restraints weight = 15492.179| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.96 r_work: 0.3957 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8920 Z= 0.217 Angle : 0.627 12.191 12149 Z= 0.316 Chirality : 0.047 0.263 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.995 57.029 1242 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.32 % Favored : 89.59 % Rotamer: Outliers : 5.52 % Allowed : 17.98 % Favored : 76.51 % 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: -3.51 (0.23), residues: 1114 helix: -3.57 (0.65), residues: 31 sheet: -1.79 (0.30), residues: 288 loop : -2.68 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.003 0.000 HIS A 67 PHE 0.018 0.001 PHE A 497 TYR 0.017 0.001 TYR C 50 ARG 0.003 0.000 ARG A 457 *********************** 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 295 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7326 (mm) REVERT: A 60 PHE cc_start: 0.7156 (m-80) cc_final: 0.6704 (m-80) REVERT: A 82 ASN cc_start: 0.7095 (m-40) cc_final: 0.6754 (m-40) REVERT: A 98 LYS cc_start: 0.7187 (mtmm) cc_final: 0.6925 (mppt) REVERT: A 266 TYR cc_start: 0.3500 (m-10) cc_final: 0.2859 (m-10) REVERT: A 310 LYS cc_start: 0.7782 (mtpp) cc_final: 0.7574 (tttp) REVERT: A 320 VAL cc_start: 0.7610 (m) cc_final: 0.7382 (m) REVERT: A 349 SER cc_start: 0.8736 (m) cc_final: 0.8486 (m) REVERT: A 355 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7451 (ttt180) REVERT: A 378 LYS cc_start: 0.7985 (pttm) cc_final: 0.7699 (pttm) REVERT: A 402 ILE cc_start: 0.7411 (tp) cc_final: 0.7145 (tt) REVERT: A 422 ASN cc_start: 0.7814 (m110) cc_final: 0.7478 (m110) REVERT: A 434 ILE cc_start: 0.8619 (mp) cc_final: 0.8375 (mt) REVERT: A 509 ARG cc_start: 0.7393 (mtt180) cc_final: 0.6966 (mmt90) REVERT: A 516 GLU cc_start: 0.7850 (tt0) cc_final: 0.7603 (tt0) REVERT: A 547 THR cc_start: 0.8051 (m) cc_final: 0.7837 (p) REVERT: A 556 ASN cc_start: 0.7889 (m-40) cc_final: 0.7644 (m-40) REVERT: A 565 PHE cc_start: 0.7075 (t80) cc_final: 0.6741 (t80) REVERT: A 583 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 586 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 612 TYR cc_start: 0.7600 (m-80) cc_final: 0.6508 (m-80) REVERT: A 624 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7105 (pt) REVERT: A 627 ASP cc_start: 0.5445 (p0) cc_final: 0.4961 (p0) REVERT: A 643 PHE cc_start: 0.5805 (m-80) cc_final: 0.5338 (m-80) REVERT: A 656 VAL cc_start: 0.7196 (t) cc_final: 0.6943 (p) REVERT: B 74 THR cc_start: 0.8167 (m) cc_final: 0.7914 (t) REVERT: B 108 ARG cc_start: 0.7832 (mmt90) cc_final: 0.7498 (mmt90) REVERT: B 147 GLN cc_start: 0.7029 (tm-30) cc_final: 0.6775 (tm-30) REVERT: C 75 LYS cc_start: 0.8812 (ptmt) cc_final: 0.8101 (ptpp) REVERT: C 77 GLN cc_start: 0.8422 (pt0) cc_final: 0.8198 (pt0) REVERT: C 109 MET cc_start: 0.8229 (mmt) cc_final: 0.7871 (mtm) REVERT: C 120 VAL cc_start: 0.8545 (t) cc_final: 0.8329 (m) outliers start: 54 outliers final: 38 residues processed: 269 average time/residue: 0.2372 time to fit residues: 84.4486 Evaluate side-chains 268 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 503 VAL 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 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 97 THR 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 C residue 18 LEU 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 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.3980 chunk 14 optimal weight: 0.0970 chunk 109 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 280 ASN A 317 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.198487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166754 restraints weight = 15496.440| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 3.93 r_work: 0.3997 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8920 Z= 0.165 Angle : 0.653 25.677 12149 Z= 0.322 Chirality : 0.047 0.351 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.917 55.819 1242 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.25 % Favored : 90.66 % Rotamer: Outliers : 4.60 % Allowed : 19.10 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.23), residues: 1114 helix: -3.49 (0.68), residues: 31 sheet: -1.60 (0.31), residues: 264 loop : -2.46 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 34 HIS 0.003 0.000 HIS A 67 PHE 0.016 0.001 PHE A 562 TYR 0.018 0.001 TYR C 50 ARG 0.005 0.000 ARG A 246 *********************** 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 282 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.7500 (t0) cc_final: 0.7231 (m-40) REVERT: A 57 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7453 (mm) REVERT: A 60 PHE cc_start: 0.6995 (m-80) cc_final: 0.6651 (m-80) REVERT: A 82 ASN cc_start: 0.6864 (m-40) cc_final: 0.6504 (m-40) REVERT: A 98 LYS cc_start: 0.7114 (mtmm) cc_final: 0.6802 (mppt) REVERT: A 246 ARG cc_start: 0.7331 (mtm110) cc_final: 0.6498 (ptm-80) REVERT: A 266 TYR cc_start: 0.3145 (m-10) cc_final: 0.2578 (m-10) REVERT: A 355 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7370 (ttt180) REVERT: A 378 LYS cc_start: 0.7830 (pttm) cc_final: 0.7605 (pttm) REVERT: A 402 ILE cc_start: 0.7193 (tp) cc_final: 0.6930 (tt) REVERT: A 420 ASP cc_start: 0.7456 (t70) cc_final: 0.7040 (t0) REVERT: A 422 ASN cc_start: 0.7799 (m-40) cc_final: 0.7467 (m-40) REVERT: A 434 ILE cc_start: 0.8541 (mp) cc_final: 0.8292 (mt) REVERT: A 466 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7905 (ptm160) REVERT: A 478 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8529 (tptp) REVERT: A 509 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6915 (mmt90) REVERT: A 516 GLU cc_start: 0.7786 (tt0) cc_final: 0.7564 (tt0) REVERT: A 523 THR cc_start: 0.8144 (p) cc_final: 0.7869 (p) REVERT: A 529 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7428 (mmmm) REVERT: A 556 ASN cc_start: 0.7862 (m-40) cc_final: 0.7659 (m-40) REVERT: A 565 PHE cc_start: 0.6949 (t80) cc_final: 0.6594 (t80) REVERT: A 583 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 586 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: A 624 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7123 (pt) REVERT: A 627 ASP cc_start: 0.5830 (p0) cc_final: 0.5358 (p0) REVERT: A 629 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 643 PHE cc_start: 0.5721 (m-80) cc_final: 0.5287 (m-80) REVERT: A 656 VAL cc_start: 0.7183 (t) cc_final: 0.6897 (p) REVERT: B 9 SER cc_start: 0.8229 (m) cc_final: 0.7906 (p) REVERT: B 108 ARG cc_start: 0.7786 (mmt90) cc_final: 0.7446 (mmt90) REVERT: B 179 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6812 (tm) REVERT: C 109 MET cc_start: 0.8175 (mmt) cc_final: 0.7860 (mtm) outliers start: 45 outliers final: 31 residues processed: 265 average time/residue: 0.2465 time to fit residues: 86.6066 Evaluate side-chains 264 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 560 LEU 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 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 629 LEU 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 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 20 LEU 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 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.196142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.164528 restraints weight = 15441.022| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 3.94 r_work: 0.3961 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8920 Z= 0.198 Angle : 0.670 23.043 12149 Z= 0.328 Chirality : 0.048 0.345 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.839 55.516 1238 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.23 % Favored : 89.68 % Rotamer: Outliers : 4.80 % Allowed : 18.69 % Favored : 76.51 % 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: -3.15 (0.23), residues: 1114 helix: -3.35 (0.69), residues: 36 sheet: -1.45 (0.30), residues: 276 loop : -2.45 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 34 HIS 0.006 0.001 HIS A 70 PHE 0.017 0.001 PHE A 497 TYR 0.020 0.001 TYR C 50 ARG 0.005 0.001 ARG B 24 *********************** 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 291 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5552 (tp) REVERT: A 57 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7750 (mm) REVERT: A 60 PHE cc_start: 0.7036 (m-80) cc_final: 0.6678 (m-80) REVERT: A 70 HIS cc_start: 0.5138 (p-80) cc_final: 0.4738 (p-80) REVERT: A 82 ASN cc_start: 0.6973 (m-40) cc_final: 0.6591 (m-40) REVERT: A 89 ASP cc_start: 0.3319 (OUTLIER) cc_final: 0.2901 (m-30) REVERT: A 98 LYS cc_start: 0.7158 (mtmm) cc_final: 0.6852 (mppt) REVERT: A 236 THR cc_start: 0.7949 (m) cc_final: 0.7459 (t) REVERT: A 246 ARG cc_start: 0.7502 (mtm110) cc_final: 0.6604 (ptm-80) REVERT: A 266 TYR cc_start: 0.3354 (m-10) cc_final: 0.2737 (m-10) REVERT: A 355 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7401 (ttt180) REVERT: A 364 ASP cc_start: 0.7405 (t70) cc_final: 0.7034 (t0) REVERT: A 402 ILE cc_start: 0.7270 (tp) cc_final: 0.7014 (tt) REVERT: A 422 ASN cc_start: 0.7853 (m-40) cc_final: 0.7571 (m-40) REVERT: A 434 ILE cc_start: 0.8604 (mp) cc_final: 0.8326 (mt) REVERT: A 455 LEU cc_start: 0.8325 (tp) cc_final: 0.8054 (tt) REVERT: A 509 ARG cc_start: 0.7358 (mtt180) cc_final: 0.6932 (mmt90) REVERT: A 516 GLU cc_start: 0.7786 (tt0) cc_final: 0.7522 (tt0) REVERT: A 523 THR cc_start: 0.8184 (p) cc_final: 0.7869 (p) REVERT: A 565 PHE cc_start: 0.7030 (t80) cc_final: 0.6756 (t80) REVERT: A 578 ASP cc_start: 0.7971 (m-30) cc_final: 0.7552 (m-30) REVERT: A 583 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 586 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: A 624 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7274 (pt) REVERT: A 627 ASP cc_start: 0.5475 (p0) cc_final: 0.4953 (p0) REVERT: A 629 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7314 (mt) REVERT: A 643 PHE cc_start: 0.5786 (m-80) cc_final: 0.5427 (m-80) REVERT: A 656 VAL cc_start: 0.7177 (t) cc_final: 0.6873 (p) REVERT: B 9 SER cc_start: 0.8180 (m) cc_final: 0.7861 (p) REVERT: B 108 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7459 (mmt90) REVERT: B 179 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6880 (tm) REVERT: C 75 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8290 (ptpp) REVERT: C 109 MET cc_start: 0.8200 (mmt) cc_final: 0.7854 (mtm) REVERT: C 201 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7375 (tm-30) outliers start: 47 outliers final: 37 residues processed: 271 average time/residue: 0.2952 time to fit residues: 107.8437 Evaluate side-chains 283 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU 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 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 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU 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 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 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 629 LEU 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 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 18 LEU 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 Chi-restraints excluded: chain C residue 220 VAL 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: 4.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 32 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** B 27 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 = 0.4480 r_free = 0.4480 target = 0.194960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.163306 restraints weight = 15780.153| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 3.96 r_work: 0.3956 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8920 Z= 0.184 Angle : 0.663 19.383 12149 Z= 0.325 Chirality : 0.047 0.316 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.832 55.369 1238 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.31 % Rotamer: Outliers : 4.90 % Allowed : 19.00 % Favored : 76.10 % 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: -3.00 (0.24), residues: 1114 helix: -3.43 (0.81), residues: 30 sheet: -1.42 (0.29), residues: 300 loop : -2.31 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 34 HIS 0.002 0.000 HIS B 198 PHE 0.015 0.001 PHE C 78 TYR 0.018 0.001 TYR C 50 ARG 0.006 0.001 ARG B 96 *********************** 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 290 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.7808 (t0) cc_final: 0.7603 (t0) REVERT: A 55 LEU cc_start: 0.7378 (mp) cc_final: 0.6648 (mp) REVERT: A 57 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 60 PHE cc_start: 0.7008 (m-80) cc_final: 0.6661 (m-80) REVERT: A 70 HIS cc_start: 0.4974 (p-80) cc_final: 0.4525 (p-80) REVERT: A 82 ASN cc_start: 0.7048 (m-40) cc_final: 0.6646 (m-40) REVERT: A 98 LYS cc_start: 0.7105 (mtmm) cc_final: 0.6775 (mppt) REVERT: A 236 THR cc_start: 0.7934 (m) cc_final: 0.7442 (t) REVERT: A 266 TYR cc_start: 0.3415 (m-10) cc_final: 0.2658 (m-10) REVERT: A 355 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7486 (ttt180) REVERT: A 364 ASP cc_start: 0.7382 (t70) cc_final: 0.7029 (t0) REVERT: A 402 ILE cc_start: 0.7248 (tp) cc_final: 0.6990 (tt) REVERT: A 434 ILE cc_start: 0.8579 (mp) cc_final: 0.8289 (mt) REVERT: A 451 TYR cc_start: 0.8329 (m-10) cc_final: 0.7842 (m-80) REVERT: A 455 LEU cc_start: 0.8354 (tp) cc_final: 0.8061 (tt) REVERT: A 509 ARG cc_start: 0.7406 (mtt180) cc_final: 0.6990 (mmt90) REVERT: A 516 GLU cc_start: 0.7790 (tt0) cc_final: 0.7554 (tt0) REVERT: A 523 THR cc_start: 0.8164 (p) cc_final: 0.7853 (p) REVERT: A 578 ASP cc_start: 0.8000 (m-30) cc_final: 0.7610 (m-30) REVERT: A 583 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 586 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: A 624 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7329 (pt) REVERT: A 629 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7244 (mt) REVERT: A 643 PHE cc_start: 0.5947 (m-80) cc_final: 0.5487 (m-80) REVERT: A 656 VAL cc_start: 0.7188 (t) cc_final: 0.6886 (p) REVERT: B 9 SER cc_start: 0.8135 (m) cc_final: 0.7820 (p) REVERT: B 108 ARG cc_start: 0.7830 (mmt90) cc_final: 0.7499 (mmt90) REVERT: B 179 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6813 (tm) REVERT: B 181 LEU cc_start: 0.8360 (mt) cc_final: 0.8025 (tp) REVERT: C 75 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8330 (ptpp) REVERT: C 109 MET cc_start: 0.8192 (mmt) cc_final: 0.7881 (mtm) outliers start: 48 outliers final: 40 residues processed: 269 average time/residue: 0.2901 time to fit residues: 104.4050 Evaluate side-chains 283 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 91 VAL 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 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU 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 432 CYS 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 572 THR 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 629 LEU 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 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 12 VAL 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 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 0.0170 chunk 47 optimal weight: 0.0030 chunk 31 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.4028 ------------------------------------------------------------------------------- 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 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.196947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.165023 restraints weight = 15780.536| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 4.03 r_work: 0.3961 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8920 Z= 0.171 Angle : 0.663 19.873 12149 Z= 0.326 Chirality : 0.047 0.307 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.797 55.256 1238 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.31 % Rotamer: Outliers : 5.01 % Allowed : 18.79 % Favored : 76.20 % 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: -2.87 (0.24), residues: 1114 helix: -3.56 (0.76), residues: 30 sheet: -1.29 (0.30), residues: 296 loop : -2.24 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 148 HIS 0.002 0.000 HIS B 198 PHE 0.031 0.001 PHE A 565 TYR 0.019 0.001 TYR C 50 ARG 0.007 0.001 ARG A 246 *********************** 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 286 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5541 (tp) REVERT: A 57 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7483 (mm) REVERT: A 60 PHE cc_start: 0.6982 (m-80) cc_final: 0.6695 (m-80) REVERT: A 70 HIS cc_start: 0.4806 (p-80) cc_final: 0.4407 (p-80) REVERT: A 82 ASN cc_start: 0.7094 (m-40) cc_final: 0.6674 (m-40) REVERT: A 89 ASP cc_start: 0.3335 (OUTLIER) cc_final: 0.2945 (m-30) REVERT: A 98 LYS cc_start: 0.7278 (mtmm) cc_final: 0.6968 (mppt) REVERT: A 236 THR cc_start: 0.7909 (m) cc_final: 0.7419 (t) REVERT: A 246 ARG cc_start: 0.7512 (mtm110) cc_final: 0.6718 (ptm-80) REVERT: A 266 TYR cc_start: 0.3289 (m-10) cc_final: 0.2587 (m-10) REVERT: A 355 ARG cc_start: 0.7780 (ttt180) cc_final: 0.7469 (ttt180) REVERT: A 402 ILE cc_start: 0.7167 (tp) cc_final: 0.6898 (tt) REVERT: A 420 ASP cc_start: 0.7406 (t70) cc_final: 0.6912 (t0) REVERT: A 434 ILE cc_start: 0.8471 (mp) cc_final: 0.8203 (mt) REVERT: A 451 TYR cc_start: 0.8321 (m-10) cc_final: 0.7910 (m-80) REVERT: A 455 LEU cc_start: 0.8308 (tp) cc_final: 0.8028 (tt) REVERT: A 509 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6994 (mmt90) REVERT: A 523 THR cc_start: 0.8132 (p) cc_final: 0.7829 (p) REVERT: A 578 ASP cc_start: 0.8023 (m-30) cc_final: 0.7643 (m-30) REVERT: A 583 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7431 (mt-10) REVERT: A 586 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: A 612 TYR cc_start: 0.7579 (m-80) cc_final: 0.6881 (m-80) REVERT: A 627 ASP cc_start: 0.5742 (p0) cc_final: 0.5324 (p0) REVERT: A 629 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7248 (mt) REVERT: A 643 PHE cc_start: 0.6020 (m-80) cc_final: 0.5504 (m-80) REVERT: A 656 VAL cc_start: 0.7151 (t) cc_final: 0.6829 (p) REVERT: B 9 SER cc_start: 0.8133 (m) cc_final: 0.7829 (p) REVERT: B 108 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7479 (mmt90) REVERT: B 179 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6792 (tm) REVERT: B 181 LEU cc_start: 0.8374 (mt) cc_final: 0.8053 (tp) REVERT: C 94 TYR cc_start: 0.8339 (m-80) cc_final: 0.8095 (m-80) REVERT: C 109 MET cc_start: 0.8227 (mmt) cc_final: 0.7881 (mtm) outliers start: 49 outliers final: 38 residues processed: 265 average time/residue: 0.2440 time to fit residues: 87.2092 Evaluate side-chains 281 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 49 LEU 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 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU 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 535 LYS Chi-restraints excluded: chain A residue 546 LEU 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 629 LEU 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 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR 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 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 72 optimal weight: 0.0030 chunk 80 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 53 optimal weight: 0.0670 overall best weight: 0.1686 ------------------------------------------------------------------------------- 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 690 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 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 = 0.4517 r_free = 0.4517 target = 0.198708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.167175 restraints weight = 15701.593| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 4.02 r_work: 0.3998 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8920 Z= 0.157 Angle : 0.671 19.640 12149 Z= 0.331 Chirality : 0.047 0.338 1355 Planarity : 0.005 0.060 1563 Dihedral : 5.730 54.777 1238 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer: Outliers : 4.70 % Allowed : 19.41 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.24), residues: 1114 helix: -3.51 (0.77), residues: 30 sheet: -1.17 (0.29), residues: 301 loop : -2.17 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 148 HIS 0.003 0.000 HIS B 198 PHE 0.025 0.001 PHE A 565 TYR 0.018 0.001 TYR C 50 ARG 0.007 0.000 ARG A 246 *********************** 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 284 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.899 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 49 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5471 (tp) REVERT: A 60 PHE cc_start: 0.6860 (m-80) cc_final: 0.6635 (m-80) REVERT: A 70 HIS cc_start: 0.4715 (p-80) cc_final: 0.4244 (p-80) REVERT: A 82 ASN cc_start: 0.7007 (m-40) cc_final: 0.6589 (m-40) REVERT: A 89 ASP cc_start: 0.2861 (OUTLIER) cc_final: 0.2527 (m-30) REVERT: A 98 LYS cc_start: 0.7213 (mtmm) cc_final: 0.6860 (mppt) REVERT: A 236 THR cc_start: 0.7745 (m) cc_final: 0.7270 (t) REVERT: A 246 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6734 (ptm-80) REVERT: A 266 TYR cc_start: 0.2997 (m-10) cc_final: 0.2504 (m-10) REVERT: A 355 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7389 (ttt180) REVERT: A 420 ASP cc_start: 0.7272 (t70) cc_final: 0.6839 (t0) REVERT: A 434 ILE cc_start: 0.8426 (mp) cc_final: 0.8144 (mt) REVERT: A 442 ASP cc_start: 0.7326 (m-30) cc_final: 0.6750 (m-30) REVERT: A 451 TYR cc_start: 0.8325 (m-10) cc_final: 0.7907 (m-80) REVERT: A 455 LEU cc_start: 0.8260 (tp) cc_final: 0.8024 (tt) REVERT: A 478 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8525 (tptp) REVERT: A 509 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6772 (mmt90) REVERT: A 516 GLU cc_start: 0.7717 (tt0) cc_final: 0.7466 (tt0) REVERT: A 523 THR cc_start: 0.8037 (p) cc_final: 0.7746 (p) REVERT: A 583 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 586 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: A 612 TYR cc_start: 0.7559 (m-80) cc_final: 0.6774 (m-80) REVERT: A 627 ASP cc_start: 0.5780 (p0) cc_final: 0.5479 (p0) REVERT: A 629 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7232 (mt) REVERT: A 643 PHE cc_start: 0.5999 (m-80) cc_final: 0.5488 (m-80) REVERT: A 656 VAL cc_start: 0.7134 (t) cc_final: 0.6812 (p) REVERT: B 9 SER cc_start: 0.8141 (m) cc_final: 0.7828 (p) REVERT: B 108 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7501 (mmt90) REVERT: B 179 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6748 (tm) REVERT: B 181 LEU cc_start: 0.8396 (mt) cc_final: 0.8071 (tp) REVERT: C 75 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8271 (ptpp) REVERT: C 109 MET cc_start: 0.8195 (mmt) cc_final: 0.7848 (mtm) outliers start: 46 outliers final: 35 residues processed: 263 average time/residue: 0.2294 time to fit residues: 80.4979 Evaluate side-chains 272 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 ASP 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 171 VAL 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 349 SER 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 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 629 LEU 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 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 35 THR 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 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 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 A 540 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.187415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155186 restraints weight = 15611.186| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.91 r_work: 0.3851 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 8920 Z= 0.416 Angle : 0.832 20.634 12149 Z= 0.418 Chirality : 0.054 0.348 1355 Planarity : 0.006 0.063 1563 Dihedral : 6.593 55.426 1238 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.30 % Favored : 87.43 % Rotamer: Outliers : 4.09 % Allowed : 20.02 % 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: -3.06 (0.24), residues: 1114 helix: -3.65 (0.57), residues: 42 sheet: -1.32 (0.30), residues: 308 loop : -2.39 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 34 HIS 0.007 0.001 HIS A 70 PHE 0.022 0.002 PHE A 562 TYR 0.023 0.002 TYR C 50 ARG 0.009 0.001 ARG A 466 ********************** 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 289 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7263 (m-80) cc_final: 0.6919 (m-80) REVERT: A 57 LEU cc_start: 0.8438 (mm) cc_final: 0.7630 (mm) REVERT: A 60 PHE cc_start: 0.7259 (m-80) cc_final: 0.6800 (m-80) REVERT: A 70 HIS cc_start: 0.4959 (p-80) cc_final: 0.4179 (p-80) REVERT: A 89 ASP cc_start: 0.4162 (OUTLIER) cc_final: 0.3649 (m-30) REVERT: A 98 LYS cc_start: 0.7509 (mtmm) cc_final: 0.7110 (mppt) REVERT: A 236 THR cc_start: 0.8096 (m) cc_final: 0.7595 (t) REVERT: A 265 TYR cc_start: 0.6233 (m-80) cc_final: 0.5681 (m-80) REVERT: A 266 TYR cc_start: 0.4362 (m-10) cc_final: 0.4096 (m-10) REVERT: A 299 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7360 (p) REVERT: A 320 VAL cc_start: 0.7791 (m) cc_final: 0.7054 (p) REVERT: A 355 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7631 (ttt180) REVERT: A 364 ASP cc_start: 0.7466 (t70) cc_final: 0.7057 (t0) REVERT: A 392 PHE cc_start: 0.7504 (m-80) cc_final: 0.7191 (m-80) REVERT: A 402 ILE cc_start: 0.7632 (tp) cc_final: 0.7348 (tt) REVERT: A 434 ILE cc_start: 0.8639 (mp) cc_final: 0.8351 (mt) REVERT: A 451 TYR cc_start: 0.8446 (m-10) cc_final: 0.8115 (m-80) REVERT: A 455 LEU cc_start: 0.8453 (tp) cc_final: 0.8110 (tt) REVERT: A 523 THR cc_start: 0.8286 (p) cc_final: 0.8064 (p) REVERT: A 529 LYS cc_start: 0.8375 (mmmm) cc_final: 0.7867 (mmmm) REVERT: A 551 VAL cc_start: 0.8490 (m) cc_final: 0.8215 (p) REVERT: A 565 PHE cc_start: 0.7319 (t80) cc_final: 0.7101 (t80) REVERT: A 578 ASP cc_start: 0.8172 (m-30) cc_final: 0.7831 (m-30) REVERT: A 583 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 586 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: A 612 TYR cc_start: 0.7773 (m-80) cc_final: 0.7025 (m-80) REVERT: A 624 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7413 (pp) REVERT: A 627 ASP cc_start: 0.5745 (p0) cc_final: 0.4990 (p0) REVERT: A 629 LEU cc_start: 0.7762 (mm) cc_final: 0.7432 (mt) REVERT: A 656 VAL cc_start: 0.7168 (t) cc_final: 0.6829 (p) REVERT: B 9 SER cc_start: 0.8137 (m) cc_final: 0.7823 (p) REVERT: B 71 PHE cc_start: 0.8451 (m-80) cc_final: 0.8237 (m-80) REVERT: B 74 THR cc_start: 0.8551 (m) cc_final: 0.8292 (t) REVERT: B 97 THR cc_start: 0.8806 (t) cc_final: 0.8497 (p) REVERT: B 108 ARG cc_start: 0.7876 (mmt90) cc_final: 0.7592 (mmt90) REVERT: B 142 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7513 (ptp90) REVERT: B 179 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6892 (tm) REVERT: C 24 VAL cc_start: 0.8224 (t) cc_final: 0.8016 (p) REVERT: C 35 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (t) REVERT: C 68 THR cc_start: 0.8861 (p) cc_final: 0.8602 (t) REVERT: C 75 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8468 (ptpp) REVERT: C 83 SER cc_start: 0.8524 (t) cc_final: 0.8263 (p) REVERT: C 187 LEU cc_start: 0.7970 (pp) cc_final: 0.7629 (pt) outliers start: 40 outliers final: 29 residues processed: 270 average time/residue: 0.2252 time to fit residues: 81.9225 Evaluate side-chains 282 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE 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 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 124 GLN 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 B residue 179 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 35 THR 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 192 THR Chi-restraints excluded: chain C residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 chunk 60 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 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** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 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 = 0.4396 r_free = 0.4396 target = 0.187140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154901 restraints weight = 15440.099| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.90 r_work: 0.3857 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.5332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 8920 Z= 0.408 Angle : 1.152 59.166 12149 Z= 0.658 Chirality : 0.062 1.144 1355 Planarity : 0.008 0.225 1563 Dihedral : 6.735 55.706 1237 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.39 % Favored : 87.34 % Rotamer: Outliers : 3.98 % Allowed : 21.04 % Favored : 74.97 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.24), residues: 1114 helix: -3.90 (0.55), residues: 42 sheet: -1.34 (0.30), residues: 308 loop : -2.39 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 34 HIS 0.016 0.002 HIS A 245 PHE 0.019 0.002 PHE A 497 TYR 0.036 0.002 TYR C 99 ARG 0.027 0.001 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5252.37 seconds wall clock time: 92 minutes 1.82 seconds (5521.82 seconds total)