Starting phenix.real_space_refine on Thu Feb 13 04:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jio_36322/02_2025/8jio_36322.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jio_36322/02_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_36322/02_2025/8jio_36322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jio_36322/02_2025/8jio_36322.map" model { file = "/net/cci-nas-00/data/ceres_data/8jio_36322/02_2025/8jio_36322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jio_36322/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.36, per 1000 atoms: 0.62 Number of scatterers: 8698 At special positions: 0 Unit cell: (117.432, 91.336, 152.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1688 8.00 N 1452 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 1.0 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: 0.95 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: 2.45 Time building geometry restraints manager: 2.28 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.070 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- 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 : 0.998 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: 0.2259 time to fit residues: 90.0608 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 : 0.919 ------------------------------------------------------------------------------- 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 = 0.167085 restraints weight = 15460.628| |-----------------------------------------------------------------------------| 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: 0.6717 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 : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.3199 (OUTLIER) cc_final: 0.2993 (m) REVERT: A 60 PHE cc_start: 0.7343 (m-80) cc_final: 0.6734 (m-80) REVERT: A 82 ASN cc_start: 0.7046 (m-40) cc_final: 0.6822 (m-40) REVERT: A 202 LYS cc_start: 0.5979 (mttt) cc_final: 0.5140 (mtmm) REVERT: A 317 ASN cc_start: 0.6636 (m110) cc_final: 0.6348 (m110) REVERT: A 320 VAL cc_start: 0.7835 (m) cc_final: 0.7102 (p) REVERT: A 355 ARG cc_start: 0.7839 (ttt180) cc_final: 0.7484 (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 434 ILE cc_start: 0.8677 (mp) cc_final: 0.8405 (mt) REVERT: A 487 ASN cc_start: 0.7852 (m-40) cc_final: 0.7562 (m-40) REVERT: A 509 ARG cc_start: 0.7338 (mtt180) cc_final: 0.6900 (mmt90) REVERT: A 547 THR cc_start: 0.8108 (m) cc_final: 0.7883 (p) REVERT: A 556 ASN cc_start: 0.8046 (m-40) cc_final: 0.7792 (m-40) REVERT: A 562 PHE cc_start: 0.7364 (m-10) cc_final: 0.7034 (m-80) REVERT: A 565 PHE cc_start: 0.7052 (t80) cc_final: 0.6792 (t80) REVERT: A 578 ASP cc_start: 0.8003 (m-30) cc_final: 0.7479 (m-30) REVERT: A 583 GLU cc_start: 0.7844 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 584 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5369 (pt) REVERT: A 586 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: A 612 TYR cc_start: 0.7420 (m-80) cc_final: 0.6364 (m-80) REVERT: A 624 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6793 (pt) REVERT: A 628 GLN cc_start: 0.6335 (mp10) cc_final: 0.5809 (mp10) REVERT: A 643 PHE cc_start: 0.5975 (m-80) cc_final: 0.5458 (m-80) REVERT: B 24 ARG cc_start: 0.7910 (mtp-110) cc_final: 0.7434 (mtp85) REVERT: B 108 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7449 (mmt90) REVERT: B 123 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 147 GLN cc_start: 0.7052 (tm-30) cc_final: 0.6655 (tm-30) REVERT: B 177 SER cc_start: 0.7769 (m) cc_final: 0.7526 (p) REVERT: C 54 THR cc_start: 0.8474 (OUTLIER) cc_final: 0.8253 (t) REVERT: C 67 VAL cc_start: 0.8831 (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: 0.8538 (t) cc_final: 0.8218 (p) REVERT: C 109 MET cc_start: 0.8287 (mmt) cc_final: 0.7873 (mtm) REVERT: C 187 LEU cc_start: 0.8010 (pp) cc_final: 0.7808 (pt) REVERT: C 201 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7430 (tm-30) outliers start: 46 outliers final: 24 residues processed: 283 average time/residue: 0.2263 time to fit residues: 86.5134 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 : 0.906 ------------------------------------------------------------------------------- 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: 7.9990 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.198698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.166658 restraints weight = 15642.677| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 4.00 r_work: 0.4000 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8920 Z= 0.200 Angle : 0.613 9.670 12149 Z= 0.307 Chirality : 0.046 0.164 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.961 58.486 1245 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 4.80 % Allowed : 16.65 % Favored : 78.55 % 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: -3.70 (0.22), residues: 1114 helix: -3.81 (0.56), residues: 31 sheet: -1.93 (0.30), residues: 283 loop : -2.81 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 148 HIS 0.003 0.000 HIS A 67 PHE 0.014 0.001 PHE A 562 TYR 0.016 0.001 TYR C 50 ARG 0.005 0.000 ARG C 66 *********************** 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 284 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 237 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6636 (mt) REVERT: A 60 PHE cc_start: 0.7205 (m-80) cc_final: 0.6672 (m-80) REVERT: A 82 ASN cc_start: 0.7123 (m-40) cc_final: 0.6877 (m-40) REVERT: A 202 LYS cc_start: 0.6046 (mttt) cc_final: 0.5141 (mtmt) REVERT: A 298 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 355 ARG cc_start: 0.7740 (ttt180) cc_final: 0.7273 (ttt180) REVERT: A 360 ASN cc_start: 0.8016 (m-40) cc_final: 0.7792 (m-40) REVERT: A 378 LYS cc_start: 0.7980 (pttm) cc_final: 0.7679 (pttm) REVERT: A 396 TYR cc_start: 0.8489 (m-80) cc_final: 0.7992 (m-10) REVERT: A 422 ASN cc_start: 0.7703 (m110) cc_final: 0.7412 (m110) REVERT: A 434 ILE cc_start: 0.8611 (mp) cc_final: 0.8334 (mt) REVERT: A 509 ARG cc_start: 0.7367 (mtt180) cc_final: 0.6963 (mmt90) REVERT: A 547 THR cc_start: 0.8020 (m) cc_final: 0.7793 (p) REVERT: A 556 ASN cc_start: 0.7952 (m-40) cc_final: 0.7702 (m-40) REVERT: A 565 PHE cc_start: 0.7003 (t80) cc_final: 0.6605 (t80) REVERT: A 583 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7356 (mt-10) REVERT: A 586 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7229 (m-30) REVERT: A 624 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6891 (pt) REVERT: A 628 GLN cc_start: 0.6228 (mp10) cc_final: 0.5922 (mp10) REVERT: A 643 PHE cc_start: 0.5937 (m-80) cc_final: 0.5416 (m-80) REVERT: B 24 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7446 (mtp85) REVERT: B 106 ILE cc_start: 0.8608 (mp) cc_final: 0.8321 (mp) REVERT: B 108 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7415 (mmt90) REVERT: B 147 GLN cc_start: 0.6973 (tm-30) cc_final: 0.6456 (tm-30) REVERT: C 11 LEU cc_start: 0.7903 (mt) cc_final: 0.7638 (tp) REVERT: C 54 THR cc_start: 0.8429 (p) cc_final: 0.8224 (t) REVERT: C 92 VAL cc_start: 0.8568 (t) cc_final: 0.8198 (p) REVERT: C 109 MET cc_start: 0.8119 (mmt) cc_final: 0.7805 (mtm) REVERT: C 187 LEU cc_start: 0.7904 (pp) cc_final: 0.7497 (pt) outliers start: 47 outliers final: 32 residues processed: 263 average time/residue: 0.2337 time to fit residues: 81.7127 Evaluate side-chains 265 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 12 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 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: 0.5980 chunk 68 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.196727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.164904 restraints weight = 15477.635| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.96 r_work: 0.3959 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8920 Z= 0.227 Angle : 0.621 9.846 12149 Z= 0.312 Chirality : 0.046 0.192 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.993 56.852 1242 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.41 % Favored : 89.50 % Rotamer: Outliers : 5.52 % Allowed : 16.96 % Favored : 77.53 % 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: -3.53 (0.23), residues: 1114 helix: -3.40 (0.70), residues: 31 sheet: -1.83 (0.29), residues: 297 loop : -2.69 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.002 0.000 HIS B 198 PHE 0.021 0.001 PHE A 497 TYR 0.016 0.001 TYR C 50 ARG 0.008 0.001 ARG A 246 *********************** 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 296 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 242 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7832 (mt) cc_final: 0.7314 (mm) REVERT: A 60 PHE cc_start: 0.7153 (m-80) cc_final: 0.6672 (m-80) REVERT: A 82 ASN cc_start: 0.7029 (m-40) cc_final: 0.6672 (m-40) REVERT: A 98 LYS cc_start: 0.7228 (mtmm) cc_final: 0.6956 (mppt) REVERT: A 236 THR cc_start: 0.8020 (m) cc_final: 0.7646 (t) REVERT: A 269 TYR cc_start: 0.6933 (m-80) cc_final: 0.4749 (m-10) REVERT: A 310 LYS cc_start: 0.7786 (mtpp) cc_final: 0.7544 (tttp) REVERT: A 355 ARG cc_start: 0.7759 (ttt180) cc_final: 0.7311 (ttt180) REVERT: A 360 ASN cc_start: 0.8197 (m-40) cc_final: 0.7951 (m-40) REVERT: A 378 LYS cc_start: 0.7961 (pttm) cc_final: 0.7691 (pttm) REVERT: A 396 TYR cc_start: 0.8503 (m-80) cc_final: 0.7802 (m-10) REVERT: A 402 ILE cc_start: 0.7485 (tp) cc_final: 0.7220 (tt) REVERT: A 422 ASN cc_start: 0.7796 (m110) cc_final: 0.7486 (m110) REVERT: A 434 ILE cc_start: 0.8580 (mp) cc_final: 0.8345 (mt) REVERT: A 509 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6952 (mmt90) REVERT: A 516 GLU cc_start: 0.7820 (tt0) cc_final: 0.7452 (tt0) REVERT: A 523 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7842 (p) REVERT: A 529 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7527 (mmmm) REVERT: A 547 THR cc_start: 0.8032 (m) cc_final: 0.7800 (p) REVERT: A 556 ASN cc_start: 0.7911 (m-40) cc_final: 0.7684 (m-40) REVERT: A 565 PHE cc_start: 0.7099 (t80) cc_final: 0.6830 (t80) REVERT: A 583 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 586 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 612 TYR cc_start: 0.7567 (m-80) cc_final: 0.6484 (m-80) REVERT: A 624 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7090 (pt) REVERT: A 627 ASP cc_start: 0.5730 (p0) cc_final: 0.5316 (p0) REVERT: A 629 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7286 (mt) REVERT: A 643 PHE cc_start: 0.5770 (m-80) cc_final: 0.5305 (m-80) REVERT: A 656 VAL cc_start: 0.7117 (t) cc_final: 0.6859 (p) REVERT: B 74 THR cc_start: 0.8174 (m) cc_final: 0.7913 (t) REVERT: B 108 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7475 (mmt90) REVERT: B 147 GLN cc_start: 0.7060 (tm-30) cc_final: 0.6820 (tm-30) REVERT: C 109 MET cc_start: 0.8211 (mmt) cc_final: 0.7867 (mtm) REVERT: C 120 VAL cc_start: 0.8550 (t) cc_final: 0.8334 (m) outliers start: 54 outliers final: 36 residues processed: 272 average time/residue: 0.2379 time to fit residues: 85.8341 Evaluate side-chains 268 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 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 495 TYR Chi-restraints excluded: chain A residue 503 VAL 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 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 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 192 THR 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: 0.9990 chunk 14 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 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 = 0.195621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163423 restraints weight = 15366.225| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 3.91 r_work: 0.3948 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8920 Z= 0.211 Angle : 0.632 16.091 12149 Z= 0.315 Chirality : 0.046 0.310 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.046 55.942 1242 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.96 % Favored : 89.95 % Rotamer: Outliers : 5.11 % Allowed : 18.18 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.23), residues: 1114 helix: -3.21 (0.74), residues: 36 sheet: -1.70 (0.29), residues: 298 loop : -2.57 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.002 0.000 HIS B 198 PHE 0.018 0.001 PHE A 562 TYR 0.020 0.001 TYR C 50 ARG 0.003 0.000 ARG A 457 *********************** 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 300 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7394 (mm) REVERT: A 60 PHE cc_start: 0.7068 (m-80) cc_final: 0.6700 (m-80) REVERT: A 82 ASN cc_start: 0.7031 (m-40) cc_final: 0.6654 (m-40) REVERT: A 98 LYS cc_start: 0.7283 (mtmm) cc_final: 0.6952 (mppt) REVERT: A 310 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7561 (tttm) REVERT: A 355 ARG cc_start: 0.7718 (ttt180) cc_final: 0.7238 (ttt180) REVERT: A 360 ASN cc_start: 0.8111 (m-40) cc_final: 0.7813 (m-40) REVERT: A 378 LYS cc_start: 0.7992 (pttm) cc_final: 0.7750 (pttm) REVERT: A 396 TYR cc_start: 0.8541 (m-80) cc_final: 0.7820 (m-10) REVERT: A 402 ILE cc_start: 0.7358 (tp) cc_final: 0.7095 (tt) REVERT: A 420 ASP cc_start: 0.7526 (t70) cc_final: 0.7096 (t0) REVERT: A 422 ASN cc_start: 0.7779 (m110) cc_final: 0.7526 (m110) REVERT: A 434 ILE cc_start: 0.8619 (mp) cc_final: 0.8360 (mt) REVERT: A 455 LEU cc_start: 0.8358 (tp) cc_final: 0.8087 (tt) REVERT: A 516 GLU cc_start: 0.7760 (tt0) cc_final: 0.7398 (tt0) REVERT: A 523 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7720 (p) REVERT: A 529 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7525 (mmmm) REVERT: A 565 PHE cc_start: 0.7047 (t80) cc_final: 0.6781 (t80) REVERT: A 578 ASP cc_start: 0.7963 (m-30) cc_final: 0.7538 (m-30) REVERT: A 583 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7301 (mt-10) REVERT: A 586 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: A 612 TYR cc_start: 0.7625 (m-80) cc_final: 0.6545 (m-80) REVERT: A 627 ASP cc_start: 0.5898 (p0) cc_final: 0.5256 (p0) REVERT: A 629 LEU cc_start: 0.7706 (mm) cc_final: 0.7257 (mt) REVERT: A 643 PHE cc_start: 0.5808 (m-80) cc_final: 0.5337 (m-80) REVERT: A 656 VAL cc_start: 0.7119 (t) cc_final: 0.6831 (p) REVERT: B 9 SER cc_start: 0.8194 (m) cc_final: 0.7931 (p) REVERT: B 108 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7526 (mmt90) REVERT: B 147 GLN cc_start: 0.7083 (tm-30) cc_final: 0.6798 (tm-30) REVERT: C 75 LYS cc_start: 0.8674 (ptmt) cc_final: 0.8153 (ptpp) outliers start: 50 outliers final: 37 residues processed: 273 average time/residue: 0.2311 time to fit residues: 83.9307 Evaluate side-chains 278 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 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 483 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 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL 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 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 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 192 THR 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: 9.9990 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 87 optimal weight: 0.0270 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 104 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.195415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.163345 restraints weight = 15511.016| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 3.93 r_work: 0.3957 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8920 Z= 0.188 Angle : 0.657 24.936 12149 Z= 0.325 Chirality : 0.047 0.364 1355 Planarity : 0.005 0.061 1563 Dihedral : 6.008 55.490 1242 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.87 % Favored : 90.04 % Rotamer: Outliers : 4.70 % Allowed : 18.69 % Favored : 76.61 % 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: -3.22 (0.23), residues: 1114 helix: -3.27 (0.73), residues: 36 sheet: -1.59 (0.29), residues: 299 loop : -2.46 (0.21), residues: 779 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 0.017 0.001 PHE A 497 TYR 0.017 0.001 TYR C 50 ARG 0.005 0.000 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 284 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 238 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5624 (tp) REVERT: A 57 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 60 PHE cc_start: 0.7053 (m-80) cc_final: 0.6701 (m-80) REVERT: A 82 ASN cc_start: 0.7102 (m-40) cc_final: 0.6702 (m-40) REVERT: A 98 LYS cc_start: 0.7219 (mtmm) cc_final: 0.6948 (mppt) REVERT: A 236 THR cc_start: 0.7938 (m) cc_final: 0.7448 (t) REVERT: A 310 LYS cc_start: 0.7793 (mtpp) cc_final: 0.7507 (tttm) REVERT: A 355 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7278 (ttt180) REVERT: A 360 ASN cc_start: 0.8087 (m-40) cc_final: 0.7796 (m-40) REVERT: A 364 ASP cc_start: 0.7411 (t70) cc_final: 0.7055 (t0) REVERT: A 378 LYS cc_start: 0.7915 (pttm) cc_final: 0.7679 (pttm) REVERT: A 396 TYR cc_start: 0.8536 (m-80) cc_final: 0.7846 (m-10) REVERT: A 402 ILE cc_start: 0.7281 (tp) cc_final: 0.7020 (tt) REVERT: A 422 ASN cc_start: 0.7833 (m-40) cc_final: 0.7524 (m-40) REVERT: A 434 ILE cc_start: 0.8600 (mp) cc_final: 0.8342 (mt) REVERT: A 455 LEU cc_start: 0.8402 (tp) cc_final: 0.8137 (tt) REVERT: A 509 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6975 (mmt90) REVERT: A 516 GLU cc_start: 0.7776 (tt0) cc_final: 0.7405 (tt0) REVERT: A 523 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 529 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7573 (mmmm) REVERT: A 578 ASP cc_start: 0.8012 (m-30) cc_final: 0.7633 (m-30) REVERT: A 583 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 586 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: A 612 TYR cc_start: 0.7610 (m-80) cc_final: 0.6484 (m-80) REVERT: A 627 ASP cc_start: 0.5679 (p0) cc_final: 0.5182 (p0) REVERT: A 629 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7231 (mt) REVERT: A 643 PHE cc_start: 0.5817 (m-80) cc_final: 0.5451 (m-80) REVERT: A 649 CYS cc_start: 0.7402 (m) cc_final: 0.6574 (t) REVERT: A 656 VAL cc_start: 0.7133 (t) cc_final: 0.6842 (p) REVERT: B 9 SER cc_start: 0.8163 (m) cc_final: 0.7880 (p) REVERT: B 108 ARG cc_start: 0.7822 (mmt90) cc_final: 0.7482 (mmt90) REVERT: B 147 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6753 (tm-30) REVERT: B 179 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6836 (tm) REVERT: B 181 LEU cc_start: 0.8345 (mt) cc_final: 0.8022 (tp) REVERT: C 75 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8314 (ptpp) REVERT: C 109 MET cc_start: 0.8182 (mmt) cc_final: 0.7915 (mtm) outliers start: 46 outliers final: 36 residues processed: 264 average time/residue: 0.2501 time to fit residues: 86.9001 Evaluate side-chains 276 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 291 CYS Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 523 THR 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 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 179 LEU Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 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: 2.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 27 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.193431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.160692 restraints weight = 15601.737| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.97 r_work: 0.3913 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8920 Z= 0.232 Angle : 0.684 24.766 12149 Z= 0.342 Chirality : 0.049 0.387 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.160 55.571 1242 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.04 % Favored : 88.78 % Rotamer: Outliers : 4.80 % Allowed : 19.10 % 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: -3.20 (0.23), residues: 1114 helix: -3.46 (0.68), residues: 35 sheet: -1.51 (0.28), residues: 309 loop : -2.49 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 34 HIS 0.002 0.000 HIS B 198 PHE 0.027 0.001 PHE A 565 TYR 0.019 0.001 TYR C 50 ARG 0.007 0.001 ARG A 246 *********************** 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 298 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7352 (mm) REVERT: A 60 PHE cc_start: 0.7095 (m-80) cc_final: 0.6740 (m-80) REVERT: A 82 ASN cc_start: 0.7192 (m-40) cc_final: 0.6755 (m-40) REVERT: A 98 LYS cc_start: 0.7267 (mtmm) cc_final: 0.6965 (mppt) REVERT: A 236 THR cc_start: 0.7923 (m) cc_final: 0.7422 (t) REVERT: A 246 ARG cc_start: 0.7626 (mtm110) cc_final: 0.6746 (ptm-80) REVERT: A 269 TYR cc_start: 0.7001 (m-80) cc_final: 0.6437 (m-10) REVERT: A 273 ARG cc_start: 0.7377 (mtt180) cc_final: 0.7165 (mtt180) REVERT: A 310 LYS cc_start: 0.7754 (mtpp) cc_final: 0.7424 (mtpp) REVERT: A 320 VAL cc_start: 0.7634 (m) cc_final: 0.6940 (p) REVERT: A 355 ARG cc_start: 0.7755 (ttt180) cc_final: 0.7296 (ttt180) REVERT: A 360 ASN cc_start: 0.8172 (m-40) cc_final: 0.7926 (m-40) REVERT: A 364 ASP cc_start: 0.7460 (t70) cc_final: 0.7118 (t0) REVERT: A 396 TYR cc_start: 0.8566 (m-80) cc_final: 0.8053 (m-10) REVERT: A 402 ILE cc_start: 0.7397 (tp) cc_final: 0.7142 (tt) REVERT: A 434 ILE cc_start: 0.8644 (mp) cc_final: 0.8342 (mt) REVERT: A 455 LEU cc_start: 0.8417 (tp) cc_final: 0.8146 (tt) REVERT: A 478 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8593 (tptp) REVERT: A 509 ARG cc_start: 0.7411 (mtt180) cc_final: 0.6975 (mmt90) REVERT: A 523 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7816 (p) REVERT: A 578 ASP cc_start: 0.8076 (m-30) cc_final: 0.7760 (m-30) REVERT: A 583 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 586 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: A 612 TYR cc_start: 0.7745 (m-80) cc_final: 0.6680 (m-80) REVERT: A 627 ASP cc_start: 0.5102 (p0) cc_final: 0.4535 (p0) REVERT: A 629 LEU cc_start: 0.7756 (mm) cc_final: 0.7324 (mt) REVERT: A 643 PHE cc_start: 0.5860 (m-80) cc_final: 0.5480 (m-80) REVERT: A 656 VAL cc_start: 0.7195 (t) cc_final: 0.6865 (p) REVERT: B 9 SER cc_start: 0.8187 (m) cc_final: 0.7908 (p) REVERT: B 108 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7526 (mmt90) REVERT: B 147 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 179 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6856 (tm) REVERT: B 181 LEU cc_start: 0.8376 (mt) cc_final: 0.8043 (tp) REVERT: C 35 THR cc_start: 0.7908 (p) cc_final: 0.7534 (p) REVERT: C 57 THR cc_start: 0.8353 (p) cc_final: 0.8120 (t) REVERT: C 75 LYS cc_start: 0.8756 (ptmt) cc_final: 0.8378 (ptpp) REVERT: C 99 TYR cc_start: 0.8377 (t80) cc_final: 0.8108 (t80) REVERT: C 201 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7303 (tm-30) outliers start: 47 outliers final: 40 residues processed: 275 average time/residue: 0.2271 time to fit residues: 82.9227 Evaluate side-chains 288 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR 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 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 349 SER 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 523 THR 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 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 GLN 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 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 100 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4417 r_free = 0.4417 target = 0.189390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156625 restraints weight = 15640.630| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.94 r_work: 0.3868 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 8920 Z= 0.328 Angle : 0.754 23.162 12149 Z= 0.381 Chirality : 0.051 0.376 1355 Planarity : 0.005 0.064 1563 Dihedral : 6.431 56.190 1241 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.30 % Favored : 87.52 % Rotamer: Outliers : 5.62 % Allowed : 18.49 % 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: -3.15 (0.24), residues: 1114 helix: -3.72 (0.60), residues: 37 sheet: -1.46 (0.30), residues: 300 loop : -2.43 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 34 HIS 0.003 0.001 HIS B 198 PHE 0.019 0.002 PHE A 497 TYR 0.037 0.002 TYR C 53 ARG 0.005 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 312 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 257 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7493 (mm) REVERT: A 60 PHE cc_start: 0.7173 (m-80) cc_final: 0.6787 (m-80) REVERT: A 98 LYS cc_start: 0.7401 (mtmm) cc_final: 0.7075 (mppt) REVERT: A 265 TYR cc_start: 0.6142 (m-80) cc_final: 0.5424 (m-80) REVERT: A 269 TYR cc_start: 0.7086 (m-80) cc_final: 0.6471 (m-10) REVERT: A 310 LYS cc_start: 0.7737 (mtpp) cc_final: 0.7409 (mtpp) REVERT: A 320 VAL cc_start: 0.7772 (m) cc_final: 0.6959 (p) REVERT: A 355 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7488 (ttt180) REVERT: A 360 ASN cc_start: 0.8246 (m-40) cc_final: 0.8017 (m-40) REVERT: A 364 ASP cc_start: 0.7458 (t70) cc_final: 0.7111 (t0) REVERT: A 392 PHE cc_start: 0.7617 (m-80) cc_final: 0.7226 (m-80) REVERT: A 396 TYR cc_start: 0.8559 (m-80) cc_final: 0.7800 (m-10) REVERT: A 402 ILE cc_start: 0.7554 (tp) cc_final: 0.7281 (tt) REVERT: A 434 ILE cc_start: 0.8644 (mp) cc_final: 0.8339 (mt) REVERT: A 455 LEU cc_start: 0.8448 (tp) cc_final: 0.8131 (tt) REVERT: A 478 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8699 (tptp) REVERT: A 516 GLU cc_start: 0.7791 (tt0) cc_final: 0.7402 (tt0) REVERT: A 565 PHE cc_start: 0.7248 (t80) cc_final: 0.7022 (t80) REVERT: A 578 ASP cc_start: 0.8114 (m-30) cc_final: 0.7675 (m-30) REVERT: A 583 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7404 (mt-10) REVERT: A 586 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: A 612 TYR cc_start: 0.7907 (m-80) cc_final: 0.6822 (m-80) REVERT: A 627 ASP cc_start: 0.5659 (p0) cc_final: 0.4799 (p0) REVERT: A 629 LEU cc_start: 0.7842 (mm) cc_final: 0.7447 (mt) REVERT: A 654 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6912 (mm-30) REVERT: A 656 VAL cc_start: 0.7035 (t) cc_final: 0.6716 (p) REVERT: B 9 SER cc_start: 0.8163 (m) cc_final: 0.7904 (p) REVERT: B 74 THR cc_start: 0.8529 (m) cc_final: 0.8257 (t) REVERT: B 97 THR cc_start: 0.8815 (t) cc_final: 0.8495 (p) REVERT: B 108 ARG cc_start: 0.7942 (mmt90) cc_final: 0.7610 (mmt90) REVERT: B 147 GLN cc_start: 0.7116 (tm-30) cc_final: 0.6765 (tm-30) REVERT: B 179 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6939 (tm) REVERT: C 38 ARG cc_start: 0.8907 (ttp-170) cc_final: 0.8592 (mtp180) REVERT: C 43 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8309 (mtmt) REVERT: C 75 LYS cc_start: 0.8842 (ptmt) cc_final: 0.8514 (ptpp) REVERT: C 99 TYR cc_start: 0.8410 (t80) cc_final: 0.8186 (t80) REVERT: C 187 LEU cc_start: 0.7974 (pp) cc_final: 0.7574 (pt) outliers start: 55 outliers final: 39 residues processed: 285 average time/residue: 0.2357 time to fit residues: 89.6382 Evaluate side-chains 290 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 248 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 57 LEU Chi-restraints excluded: chain A residue 91 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 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 551 VAL 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 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 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 119 THR 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: 0.8980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN 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 27 GLN B 38 GLN ** C 164 ASN ** 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 = 0.4449 r_free = 0.4449 target = 0.192177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159166 restraints weight = 15519.839| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 4.02 r_work: 0.3902 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8920 Z= 0.221 Angle : 0.722 21.130 12149 Z= 0.358 Chirality : 0.049 0.345 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.136 55.526 1239 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.41 % Favored : 89.41 % Rotamer: Outliers : 4.70 % Allowed : 20.84 % Favored : 74.46 % 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: -3.17 (0.24), residues: 1114 helix: -3.70 (0.60), residues: 36 sheet: -1.55 (0.28), residues: 319 loop : -2.41 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 34 HIS 0.003 0.001 HIS A 245 PHE 0.017 0.001 PHE A 565 TYR 0.036 0.001 TYR C 53 ARG 0.008 0.001 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 298 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 60 PHE cc_start: 0.7089 (m-80) cc_final: 0.6686 (m-80) REVERT: A 89 ASP cc_start: 0.3903 (OUTLIER) cc_final: 0.3392 (m-30) REVERT: A 98 LYS cc_start: 0.7358 (mtmm) cc_final: 0.6983 (mppt) REVERT: A 265 TYR cc_start: 0.5992 (m-80) cc_final: 0.5207 (m-80) REVERT: A 269 TYR cc_start: 0.6980 (m-80) cc_final: 0.6395 (m-10) REVERT: A 310 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7401 (mtpp) REVERT: A 320 VAL cc_start: 0.7705 (m) cc_final: 0.6912 (p) REVERT: A 355 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7343 (ttt180) REVERT: A 360 ASN cc_start: 0.8114 (m-40) cc_final: 0.7899 (m-40) REVERT: A 364 ASP cc_start: 0.7371 (t70) cc_final: 0.7026 (t0) REVERT: A 396 TYR cc_start: 0.8538 (m-80) cc_final: 0.8039 (m-10) REVERT: A 402 ILE cc_start: 0.7367 (tp) cc_final: 0.7097 (tt) REVERT: A 434 ILE cc_start: 0.8572 (mp) cc_final: 0.8299 (mt) REVERT: A 454 ARG cc_start: 0.7746 (tpp80) cc_final: 0.7284 (tpp80) REVERT: A 455 LEU cc_start: 0.8369 (tp) cc_final: 0.8096 (tt) REVERT: A 529 LYS cc_start: 0.8347 (mmmm) cc_final: 0.7821 (mmmm) REVERT: A 565 PHE cc_start: 0.7198 (t80) cc_final: 0.6978 (t80) REVERT: A 578 ASP cc_start: 0.8066 (m-30) cc_final: 0.7821 (m-30) REVERT: A 586 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: A 612 TYR cc_start: 0.7820 (m-80) cc_final: 0.6730 (m-80) REVERT: A 627 ASP cc_start: 0.5503 (p0) cc_final: 0.4677 (p0) REVERT: A 629 LEU cc_start: 0.7790 (mm) cc_final: 0.7396 (mt) REVERT: A 654 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6792 (mm-30) REVERT: A 656 VAL cc_start: 0.7124 (t) cc_final: 0.6793 (p) REVERT: B 9 SER cc_start: 0.8128 (m) cc_final: 0.7831 (p) REVERT: B 97 THR cc_start: 0.8822 (t) cc_final: 0.8493 (p) REVERT: B 108 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7614 (mmt90) REVERT: B 147 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6711 (tm-30) REVERT: B 179 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6919 (tm) REVERT: B 181 LEU cc_start: 0.8421 (mt) cc_final: 0.8116 (tp) REVERT: C 32 TYR cc_start: 0.8299 (m-10) cc_final: 0.8051 (m-80) REVERT: C 38 ARG cc_start: 0.8823 (ttp-170) cc_final: 0.8556 (mtp180) REVERT: C 43 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8267 (mtmt) REVERT: C 99 TYR cc_start: 0.8408 (t80) cc_final: 0.8184 (t80) outliers start: 46 outliers final: 36 residues processed: 275 average time/residue: 0.2320 time to fit residues: 85.2222 Evaluate side-chains 285 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN 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 207 HIS 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 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 551 VAL 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 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 27 GLN 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 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 119 THR 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: 0.6980 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.188773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155496 restraints weight = 15566.382| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 3.98 r_work: 0.3871 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 8920 Z= 0.311 Angle : 0.762 20.718 12149 Z= 0.383 Chirality : 0.051 0.350 1355 Planarity : 0.005 0.064 1563 Dihedral : 6.327 55.494 1239 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.30 % Favored : 87.52 % Rotamer: Outliers : 4.19 % Allowed : 21.35 % Favored : 74.46 % 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: -3.13 (0.24), residues: 1114 helix: -3.76 (0.54), residues: 42 sheet: -1.36 (0.29), residues: 309 loop : -2.45 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 34 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 562 TYR 0.031 0.002 TYR C 53 ARG 0.007 0.001 ARG A 246 ********************** 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 285 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 60 PHE cc_start: 0.7175 (m-80) cc_final: 0.6759 (m-80) REVERT: A 98 LYS cc_start: 0.7538 (mtmm) cc_final: 0.7156 (mppt) REVERT: A 239 GLN cc_start: 0.7253 (mt0) cc_final: 0.6966 (tp40) REVERT: A 265 TYR cc_start: 0.6153 (m-80) cc_final: 0.5402 (m-80) REVERT: A 269 TYR cc_start: 0.7055 (m-80) cc_final: 0.6446 (m-10) REVERT: A 310 LYS cc_start: 0.7763 (mtpp) cc_final: 0.7435 (mtpp) REVERT: A 320 VAL cc_start: 0.7801 (m) cc_final: 0.6975 (p) REVERT: A 349 SER cc_start: 0.8703 (m) cc_final: 0.8197 (t) REVERT: A 355 ARG cc_start: 0.7828 (ttt180) cc_final: 0.7462 (ttt180) REVERT: A 364 ASP cc_start: 0.7390 (t70) cc_final: 0.7054 (t0) REVERT: A 392 PHE cc_start: 0.7625 (m-80) cc_final: 0.7269 (m-80) REVERT: A 396 TYR cc_start: 0.8541 (m-80) cc_final: 0.8081 (m-10) REVERT: A 402 ILE cc_start: 0.7516 (tp) cc_final: 0.7251 (tt) REVERT: A 434 ILE cc_start: 0.8595 (mp) cc_final: 0.8312 (mt) REVERT: A 455 LEU cc_start: 0.8405 (tp) cc_final: 0.8136 (tt) REVERT: A 578 ASP cc_start: 0.8078 (m-30) cc_final: 0.7827 (m-30) REVERT: A 586 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: A 612 TYR cc_start: 0.7890 (m-80) cc_final: 0.6782 (m-80) REVERT: A 627 ASP cc_start: 0.5785 (p0) cc_final: 0.4927 (p0) REVERT: A 629 LEU cc_start: 0.7894 (mm) cc_final: 0.7541 (mt) REVERT: A 649 CYS cc_start: 0.8075 (m) cc_final: 0.6755 (t) REVERT: A 654 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6790 (mm-30) REVERT: A 656 VAL cc_start: 0.7213 (t) cc_final: 0.6857 (p) REVERT: B 9 SER cc_start: 0.8146 (m) cc_final: 0.7873 (p) REVERT: B 74 THR cc_start: 0.8511 (m) cc_final: 0.8258 (t) REVERT: B 97 THR cc_start: 0.8836 (t) cc_final: 0.8509 (p) REVERT: B 108 ARG cc_start: 0.7956 (mmt90) cc_final: 0.7627 (mmt90) REVERT: B 147 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6678 (tm-30) REVERT: B 179 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6949 (tm) REVERT: B 181 LEU cc_start: 0.8473 (mt) cc_final: 0.8148 (tp) REVERT: C 38 ARG cc_start: 0.8891 (ttp-170) cc_final: 0.8627 (mtp180) REVERT: C 43 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8328 (mtmt) REVERT: C 99 TYR cc_start: 0.8408 (t80) cc_final: 0.8157 (t80) REVERT: C 187 LEU cc_start: 0.7949 (pp) cc_final: 0.7510 (pt) outliers start: 41 outliers final: 35 residues processed: 266 average time/residue: 0.2359 time to fit residues: 83.1999 Evaluate side-chains 280 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 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 551 VAL 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 624 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 VAL 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 119 THR 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: 6.9990 chunk 68 optimal weight: 0.0020 chunk 60 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4202 ------------------------------------------------------------------------------- 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 556 ASN B 89 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** 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 = 0.4462 r_free = 0.4462 target = 0.193630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.161274 restraints weight = 15552.921| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.98 r_work: 0.3924 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8920 Z= 0.197 Angle : 0.711 20.384 12149 Z= 0.354 Chirality : 0.048 0.336 1355 Planarity : 0.005 0.063 1563 Dihedral : 6.123 55.719 1239 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.61 % Favored : 90.22 % Rotamer: Outliers : 3.88 % Allowed : 22.27 % Favored : 73.85 % 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: -2.99 (0.24), residues: 1114 helix: -3.75 (0.57), residues: 36 sheet: -1.26 (0.29), residues: 310 loop : -2.36 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 34 HIS 0.003 0.001 HIS B 198 PHE 0.038 0.001 PHE A 565 TYR 0.028 0.001 TYR C 53 ARG 0.006 0.001 ARG A 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.95 seconds wall clock time: 86 minutes 58.24 seconds (5218.24 seconds total)