Starting phenix.real_space_refine on Fri Nov 15 09:21:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/11_2024/8jio_36322.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/11_2024/8jio_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/11_2024/8jio_36322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/11_2024/8jio_36322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/11_2024/8jio_36322.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jio_36322/11_2024/8jio_36322.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5524 2.51 5 N 1452 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.37, 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: 2.17 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: 1.26 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: 2.51 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.960 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.370 ------------------------------------------------------------------------------- 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 : 0.936 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: 0.2254 time to fit residues: 90.2674 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 : 0.916 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8920 Z= 0.284 Angle : 0.656 9.340 12149 Z= 0.331 Chirality : 0.047 0.193 1355 Planarity : 0.006 0.061 1563 Dihedral : 7.233 79.478 1262 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.59 % Favored : 89.32 % Rotamer: Outliers : 4.70 % Allowed : 13.07 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.22), residues: 1114 helix: -3.98 (0.48), residues: 31 sheet: -2.37 (0.27), residues: 312 loop : -2.99 (0.20), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 34 HIS 0.004 0.001 HIS A 339 PHE 0.019 0.002 PHE A 275 TYR 0.020 0.002 TYR A 313 ARG 0.011 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6758 (mt) REVERT: A 60 PHE cc_start: 0.7098 (m-80) cc_final: 0.6493 (m-80) REVERT: A 82 ASN cc_start: 0.6881 (m-40) cc_final: 0.6628 (m-40) REVERT: A 202 LYS cc_start: 0.5604 (mttt) cc_final: 0.4844 (mtmm) REVERT: A 317 ASN cc_start: 0.6330 (m110) cc_final: 0.6003 (m110) REVERT: A 320 VAL cc_start: 0.7696 (m) cc_final: 0.6977 (p) REVERT: A 355 ARG cc_start: 0.7442 (ttt180) cc_final: 0.7089 (ttt180) REVERT: A 360 ASN cc_start: 0.7977 (m-40) cc_final: 0.7761 (m-40) REVERT: A 382 VAL cc_start: 0.8316 (t) cc_final: 0.8027 (p) REVERT: A 392 PHE cc_start: 0.7330 (m-80) cc_final: 0.6929 (m-80) REVERT: A 396 TYR cc_start: 0.8390 (m-80) cc_final: 0.7975 (m-10) REVERT: A 402 ILE cc_start: 0.7477 (tp) cc_final: 0.7277 (tt) REVERT: A 434 ILE cc_start: 0.8473 (mp) cc_final: 0.8176 (mt) REVERT: A 487 ASN cc_start: 0.7625 (m-40) cc_final: 0.7338 (m-40) REVERT: A 509 ARG cc_start: 0.6983 (mtt180) cc_final: 0.6554 (mmt90) REVERT: A 547 THR cc_start: 0.8011 (m) cc_final: 0.7790 (p) REVERT: A 556 ASN cc_start: 0.7745 (m-40) cc_final: 0.7497 (m-40) REVERT: A 562 PHE cc_start: 0.7170 (m-10) cc_final: 0.6865 (m-80) REVERT: A 565 PHE cc_start: 0.6441 (t80) cc_final: 0.6210 (t80) REVERT: A 578 ASP cc_start: 0.7287 (m-30) cc_final: 0.6685 (m-30) REVERT: A 583 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6384 (mt-10) REVERT: A 584 ILE cc_start: 0.5191 (OUTLIER) cc_final: 0.4790 (pt) REVERT: A 586 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6549 (m-30) REVERT: A 612 TYR cc_start: 0.7138 (m-80) cc_final: 0.6090 (m-80) REVERT: A 624 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6562 (pt) REVERT: A 628 GLN cc_start: 0.5936 (mp10) cc_final: 0.5407 (mp10) REVERT: A 643 PHE cc_start: 0.5081 (m-80) cc_final: 0.4781 (m-80) REVERT: B 24 ARG cc_start: 0.7164 (mtp-110) cc_final: 0.6753 (mtp85) REVERT: B 42 LYS cc_start: 0.8013 (mtmp) cc_final: 0.7784 (mtmp) REVERT: B 108 ARG cc_start: 0.7164 (mmt90) cc_final: 0.6813 (mmt90) REVERT: B 123 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 147 GLN cc_start: 0.6566 (tm-30) cc_final: 0.6197 (tm-30) REVERT: B 177 SER cc_start: 0.7466 (m) cc_final: 0.7255 (p) REVERT: C 54 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8126 (t) REVERT: C 67 VAL cc_start: 0.8794 (p) cc_final: 0.8427 (m) REVERT: C 75 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8128 (ptpp) REVERT: C 92 VAL cc_start: 0.8285 (t) cc_final: 0.7968 (p) REVERT: C 116 THR cc_start: 0.8498 (p) cc_final: 0.8279 (p) REVERT: C 218 LYS cc_start: 0.7587 (mmmm) cc_final: 0.7348 (mmmm) outliers start: 46 outliers final: 24 residues processed: 283 average time/residue: 0.2287 time to fit residues: 87.7582 Evaluate side-chains 271 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU 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 55 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8920 Z= 0.207 Angle : 0.612 9.914 12149 Z= 0.308 Chirality : 0.046 0.174 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.089 58.616 1246 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 4.70 % Allowed : 16.24 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.22), residues: 1114 helix: -3.76 (0.58), residues: 31 sheet: -1.94 (0.30), residues: 282 loop : -2.82 (0.19), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 148 HIS 0.003 0.001 HIS A 67 PHE 0.013 0.001 PHE A 56 TYR 0.016 0.001 TYR C 50 ARG 0.004 0.001 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 280 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.6959 (m-80) cc_final: 0.6418 (m-80) REVERT: A 82 ASN cc_start: 0.6930 (m-40) cc_final: 0.6643 (m-40) REVERT: A 298 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7027 (mt-10) REVERT: A 355 ARG cc_start: 0.7327 (ttt180) cc_final: 0.6837 (ttt180) REVERT: A 360 ASN cc_start: 0.7856 (m-40) cc_final: 0.7649 (m-40) REVERT: A 396 TYR cc_start: 0.8395 (m-80) cc_final: 0.7929 (m-10) REVERT: A 422 ASN cc_start: 0.7344 (m110) cc_final: 0.7124 (m110) REVERT: A 434 ILE cc_start: 0.8409 (mp) cc_final: 0.8105 (mt) REVERT: A 509 ARG cc_start: 0.6992 (mtt180) cc_final: 0.6594 (mmt90) REVERT: A 547 THR cc_start: 0.7952 (m) cc_final: 0.7724 (p) REVERT: A 556 ASN cc_start: 0.7696 (m-40) cc_final: 0.7484 (m-40) REVERT: A 565 PHE cc_start: 0.6324 (t80) cc_final: 0.5977 (t80) REVERT: A 583 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 584 ILE cc_start: 0.5057 (OUTLIER) cc_final: 0.4674 (pt) REVERT: A 586 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: A 624 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6642 (pt) REVERT: A 643 PHE cc_start: 0.4990 (m-80) cc_final: 0.4705 (m-80) REVERT: B 24 ARG cc_start: 0.7092 (mtp-110) cc_final: 0.6824 (mtp85) REVERT: B 42 LYS cc_start: 0.7981 (mtmp) cc_final: 0.7751 (mtmp) REVERT: B 106 ILE cc_start: 0.8463 (mp) cc_final: 0.8137 (mp) REVERT: B 108 ARG cc_start: 0.7107 (mmt90) cc_final: 0.6752 (mmt90) REVERT: B 147 GLN cc_start: 0.6486 (tm-30) cc_final: 0.5986 (tm-30) REVERT: C 54 THR cc_start: 0.8308 (p) cc_final: 0.8098 (t) REVERT: C 116 THR cc_start: 0.8392 (p) cc_final: 0.8189 (p) REVERT: C 120 VAL cc_start: 0.8363 (t) cc_final: 0.8156 (m) outliers start: 46 outliers final: 29 residues processed: 259 average time/residue: 0.2365 time to fit residues: 81.3275 Evaluate side-chains 269 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 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 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 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 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 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 47 optimal weight: 0.0670 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 0.0670 chunk 95 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8920 Z= 0.188 Angle : 0.593 11.890 12149 Z= 0.297 Chirality : 0.045 0.163 1355 Planarity : 0.005 0.060 1563 Dihedral : 5.846 57.089 1244 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.16 % Favored : 90.75 % Rotamer: Outliers : 4.80 % Allowed : 17.47 % Favored : 77.73 % 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: -3.51 (0.23), residues: 1114 helix: -3.75 (0.59), residues: 31 sheet: -1.76 (0.29), residues: 293 loop : -2.68 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.003 0.000 ARG A 273 *********************** 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 294 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.6985 (t0) cc_final: 0.6761 (m-40) REVERT: A 60 PHE cc_start: 0.6952 (m-80) cc_final: 0.6325 (m-80) REVERT: A 82 ASN cc_start: 0.6739 (m-40) cc_final: 0.6484 (m-40) REVERT: A 98 LYS cc_start: 0.7130 (mtmm) cc_final: 0.6862 (mppt) REVERT: A 236 THR cc_start: 0.7902 (m) cc_final: 0.7513 (t) REVERT: A 298 GLU cc_start: 0.7244 (mt-10) cc_final: 0.7034 (mt-10) REVERT: A 355 ARG cc_start: 0.7328 (ttt180) cc_final: 0.6829 (ttt180) REVERT: A 357 ARG cc_start: 0.7557 (ptm160) cc_final: 0.7356 (ttp-170) REVERT: A 360 ASN cc_start: 0.7900 (m-40) cc_final: 0.7667 (m-40) REVERT: A 378 LYS cc_start: 0.7579 (pttm) cc_final: 0.7313 (pttm) REVERT: A 396 TYR cc_start: 0.8390 (m-80) cc_final: 0.7661 (m-10) REVERT: A 402 ILE cc_start: 0.7223 (tp) cc_final: 0.6943 (tt) REVERT: A 422 ASN cc_start: 0.7370 (m110) cc_final: 0.7069 (m110) REVERT: A 434 ILE cc_start: 0.8393 (mp) cc_final: 0.8067 (mt) REVERT: A 509 ARG cc_start: 0.7021 (mtt180) cc_final: 0.6624 (mmt90) REVERT: A 516 GLU cc_start: 0.7301 (tt0) cc_final: 0.6996 (tt0) REVERT: A 529 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7149 (mmmm) REVERT: A 547 THR cc_start: 0.7882 (m) cc_final: 0.7652 (p) REVERT: A 556 ASN cc_start: 0.7673 (m-40) cc_final: 0.7413 (m-40) REVERT: A 565 PHE cc_start: 0.6354 (t80) cc_final: 0.6047 (t80) REVERT: A 583 GLU cc_start: 0.7235 (mt-10) cc_final: 0.7009 (mt-10) REVERT: A 586 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: A 624 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6771 (pt) REVERT: A 627 ASP cc_start: 0.5368 (p0) cc_final: 0.4879 (p0) REVERT: A 629 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7075 (mt) REVERT: A 643 PHE cc_start: 0.4992 (m-80) cc_final: 0.4697 (m-80) REVERT: B 24 ARG cc_start: 0.7154 (mtp-110) cc_final: 0.6869 (mtp85) REVERT: B 42 LYS cc_start: 0.7889 (mtmp) cc_final: 0.7636 (mtmp) REVERT: B 106 ILE cc_start: 0.8368 (mp) cc_final: 0.8121 (mp) REVERT: B 108 ARG cc_start: 0.7099 (mmt90) cc_final: 0.6742 (mmt90) REVERT: B 147 GLN cc_start: 0.6468 (tm-30) cc_final: 0.5923 (tm-30) REVERT: C 54 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8074 (t) REVERT: C 116 THR cc_start: 0.8415 (p) cc_final: 0.8201 (p) outliers start: 47 outliers final: 36 residues processed: 268 average time/residue: 0.2472 time to fit residues: 88.5817 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 : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP 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 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 576 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 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 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 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 54 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 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 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 39 GLN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8920 Z= 0.213 Angle : 0.644 20.460 12149 Z= 0.319 Chirality : 0.047 0.319 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.939 56.380 1242 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.41 % Favored : 89.50 % Rotamer: Outliers : 5.31 % Allowed : 17.47 % Favored : 77.22 % 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: -3.33 (0.23), residues: 1114 helix: -3.50 (0.69), residues: 31 sheet: -1.59 (0.29), residues: 305 loop : -2.59 (0.20), residues: 778 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 0.028 0.001 PHE A 497 TYR 0.020 0.001 TYR C 50 ARG 0.005 0.001 ARG B 96 *********************** 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 299 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 247 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.6942 (mm) REVERT: A 60 PHE cc_start: 0.6968 (m-80) cc_final: 0.6401 (m-80) REVERT: A 82 ASN cc_start: 0.6714 (m-40) cc_final: 0.6336 (m-40) REVERT: A 98 LYS cc_start: 0.7097 (mtmm) cc_final: 0.6761 (mppt) REVERT: A 246 ARG cc_start: 0.7264 (mtm110) cc_final: 0.6384 (ptm-80) REVERT: A 355 ARG cc_start: 0.7346 (ttt180) cc_final: 0.6882 (ttt180) REVERT: A 360 ASN cc_start: 0.8002 (m-40) cc_final: 0.7736 (m-40) REVERT: A 378 LYS cc_start: 0.7695 (pttm) cc_final: 0.7335 (pttm) REVERT: A 396 TYR cc_start: 0.8408 (m-80) cc_final: 0.7673 (m-10) REVERT: A 402 ILE cc_start: 0.7172 (tp) cc_final: 0.6919 (tt) REVERT: A 422 ASN cc_start: 0.7385 (m110) cc_final: 0.7083 (m110) REVERT: A 434 ILE cc_start: 0.8425 (mp) cc_final: 0.8108 (mt) REVERT: A 509 ARG cc_start: 0.7016 (mtt180) cc_final: 0.6558 (mmt90) REVERT: A 516 GLU cc_start: 0.7340 (tt0) cc_final: 0.7063 (tt0) REVERT: A 523 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7483 (p) REVERT: A 529 LYS cc_start: 0.7710 (mmmm) cc_final: 0.7251 (mmmm) REVERT: A 552 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 556 ASN cc_start: 0.7687 (m-40) cc_final: 0.7435 (m-40) REVERT: A 565 PHE cc_start: 0.6388 (t80) cc_final: 0.6126 (t80) REVERT: A 578 ASP cc_start: 0.7259 (m-30) cc_final: 0.6761 (m-30) REVERT: A 583 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6844 (mt-10) REVERT: A 586 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: A 612 TYR cc_start: 0.7191 (m-80) cc_final: 0.6135 (m-80) REVERT: A 624 ILE cc_start: 0.7219 (OUTLIER) cc_final: 0.6924 (pt) REVERT: A 627 ASP cc_start: 0.5567 (p0) cc_final: 0.5294 (p0) REVERT: A 643 PHE cc_start: 0.4874 (m-80) cc_final: 0.4621 (m-80) REVERT: A 656 VAL cc_start: 0.7036 (t) cc_final: 0.6824 (p) REVERT: B 9 SER cc_start: 0.7923 (m) cc_final: 0.7662 (p) REVERT: B 42 LYS cc_start: 0.7977 (mtmp) cc_final: 0.7689 (mtmp) REVERT: B 108 ARG cc_start: 0.7131 (mmt90) cc_final: 0.6791 (mmt90) REVERT: B 147 GLN cc_start: 0.6626 (tm-30) cc_final: 0.6368 (tm-30) REVERT: C 75 LYS cc_start: 0.8459 (ptmt) cc_final: 0.8016 (ptpp) outliers start: 52 outliers final: 34 residues processed: 274 average time/residue: 0.2419 time to fit residues: 89.0669 Evaluate side-chains 270 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 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 349 SER 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 552 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 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 37 ILE Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8920 Z= 0.239 Angle : 0.683 23.231 12149 Z= 0.339 Chirality : 0.049 0.378 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.185 57.029 1242 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.68 % Favored : 89.23 % Rotamer: Outliers : 5.01 % Allowed : 18.79 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.23), residues: 1114 helix: -3.69 (0.61), residues: 36 sheet: -1.55 (0.29), residues: 303 loop : -2.54 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 34 HIS 0.003 0.000 HIS A 70 PHE 0.029 0.001 PHE A 497 TYR 0.019 0.001 TYR C 50 ARG 0.004 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 0.886 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: 0.7970 (OUTLIER) cc_final: 0.7008 (mm) REVERT: A 60 PHE cc_start: 0.6934 (m-80) cc_final: 0.6448 (m-80) REVERT: A 82 ASN cc_start: 0.6961 (m-40) cc_final: 0.6532 (m-40) REVERT: A 98 LYS cc_start: 0.7182 (mtmm) cc_final: 0.6859 (mppt) REVERT: A 236 THR cc_start: 0.7861 (m) cc_final: 0.7374 (t) REVERT: A 355 ARG cc_start: 0.7371 (ttt180) cc_final: 0.6930 (ttt180) REVERT: A 360 ASN cc_start: 0.8068 (m-40) cc_final: 0.7806 (m-40) REVERT: A 378 LYS cc_start: 0.7533 (pttm) cc_final: 0.7291 (pttm) REVERT: A 396 TYR cc_start: 0.8431 (m-80) cc_final: 0.7616 (m-10) REVERT: A 402 ILE cc_start: 0.7250 (tp) cc_final: 0.6994 (tt) REVERT: A 422 ASN cc_start: 0.7375 (m110) cc_final: 0.7068 (m-40) REVERT: A 434 ILE cc_start: 0.8460 (mp) cc_final: 0.8109 (mt) REVERT: A 478 LYS cc_start: 0.8787 (tptp) cc_final: 0.8571 (mmmm) REVERT: A 516 GLU cc_start: 0.7348 (tt0) cc_final: 0.6981 (tt0) REVERT: A 523 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7466 (p) REVERT: A 529 LYS cc_start: 0.7917 (mmmm) cc_final: 0.7477 (mmmm) REVERT: A 556 ASN cc_start: 0.7694 (m-40) cc_final: 0.7461 (m-40) REVERT: A 578 ASP cc_start: 0.7338 (m-30) cc_final: 0.6891 (m-30) REVERT: A 583 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6887 (mt-10) REVERT: A 586 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: A 612 TYR cc_start: 0.7399 (m-80) cc_final: 0.6259 (m-80) REVERT: A 627 ASP cc_start: 0.4916 (p0) cc_final: 0.4485 (p0) REVERT: A 629 LEU cc_start: 0.7607 (mm) cc_final: 0.7100 (mt) REVERT: A 649 CYS cc_start: 0.6952 (m) cc_final: 0.6244 (t) REVERT: A 656 VAL cc_start: 0.7099 (t) cc_final: 0.6844 (p) REVERT: B 9 SER cc_start: 0.7829 (m) cc_final: 0.7570 (p) REVERT: B 42 LYS cc_start: 0.8063 (mtmp) cc_final: 0.7787 (mtmp) REVERT: B 108 ARG cc_start: 0.7148 (mmt90) cc_final: 0.6875 (mmt90) REVERT: B 147 GLN cc_start: 0.6608 (tm-30) cc_final: 0.6296 (tm-30) REVERT: B 179 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6671 (tm) REVERT: B 181 LEU cc_start: 0.8321 (mt) cc_final: 0.8014 (tp) REVERT: C 45 LEU cc_start: 0.8552 (mm) cc_final: 0.8302 (mp) REVERT: C 75 LYS cc_start: 0.8543 (ptmt) cc_final: 0.8058 (ptpp) outliers start: 49 outliers final: 34 residues processed: 273 average time/residue: 0.2418 time to fit residues: 88.1753 Evaluate side-chains 272 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 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 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 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 11 LEU Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 119 THR 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 11 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** A 448 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8920 Z= 0.216 Angle : 0.687 21.175 12149 Z= 0.337 Chirality : 0.048 0.341 1355 Planarity : 0.005 0.062 1563 Dihedral : 6.116 56.520 1240 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.14 % Favored : 89.68 % Rotamer: Outliers : 4.60 % Allowed : 20.22 % Favored : 75.18 % 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: -3.21 (0.23), residues: 1114 helix: -3.60 (0.67), residues: 31 sheet: -1.56 (0.29), residues: 302 loop : -2.47 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 34 HIS 0.003 0.001 HIS A 67 PHE 0.024 0.001 PHE A 565 TYR 0.024 0.001 TYR C 50 ARG 0.008 0.001 ARG A 357 *********************** 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 295 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.686 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: 0.7953 (OUTLIER) cc_final: 0.6691 (mm) REVERT: A 60 PHE cc_start: 0.6910 (m-80) cc_final: 0.6455 (m-80) REVERT: A 82 ASN cc_start: 0.7123 (m-40) cc_final: 0.6662 (m-40) REVERT: A 236 THR cc_start: 0.7765 (m) cc_final: 0.7265 (t) REVERT: A 246 ARG cc_start: 0.7395 (mtm110) cc_final: 0.6512 (ptm-80) REVERT: A 269 TYR cc_start: 0.6692 (m-80) cc_final: 0.6190 (m-10) REVERT: A 273 ARG cc_start: 0.6841 (mtt180) cc_final: 0.6476 (mtt180) REVERT: A 355 ARG cc_start: 0.7363 (ttt180) cc_final: 0.6864 (ttt180) REVERT: A 360 ASN cc_start: 0.7985 (m-40) cc_final: 0.7733 (m-40) REVERT: A 364 ASP cc_start: 0.7090 (t70) cc_final: 0.6732 (t0) REVERT: A 378 LYS cc_start: 0.7524 (pttm) cc_final: 0.7288 (pttm) REVERT: A 396 TYR cc_start: 0.8388 (m-80) cc_final: 0.7908 (m-10) REVERT: A 402 ILE cc_start: 0.7191 (tp) cc_final: 0.6940 (tt) REVERT: A 422 ASN cc_start: 0.7473 (m-40) cc_final: 0.7166 (m-40) REVERT: A 434 ILE cc_start: 0.8342 (mp) cc_final: 0.8030 (mt) REVERT: A 509 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6634 (mmt90) REVERT: A 523 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7410 (p) REVERT: A 556 ASN cc_start: 0.7687 (m-40) cc_final: 0.7451 (m-40) REVERT: A 578 ASP cc_start: 0.7323 (m-30) cc_final: 0.6917 (m-30) REVERT: A 583 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 586 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: A 587 ILE cc_start: 0.8794 (mt) cc_final: 0.8573 (mt) REVERT: A 612 TYR cc_start: 0.7394 (m-80) cc_final: 0.6294 (m-80) REVERT: A 629 LEU cc_start: 0.7629 (mm) cc_final: 0.7124 (mt) REVERT: A 656 VAL cc_start: 0.7016 (t) cc_final: 0.6766 (p) REVERT: B 9 SER cc_start: 0.7824 (m) cc_final: 0.7521 (p) REVERT: B 42 LYS cc_start: 0.8073 (mtmp) cc_final: 0.7780 (mtmp) REVERT: B 108 ARG cc_start: 0.7155 (mmt90) cc_final: 0.6836 (mmt90) REVERT: B 147 GLN cc_start: 0.6518 (tm-30) cc_final: 0.6181 (tm-30) REVERT: B 179 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6701 (tm) REVERT: B 181 LEU cc_start: 0.8340 (mt) cc_final: 0.8026 (tp) REVERT: C 45 LEU cc_start: 0.8558 (mm) cc_final: 0.8317 (mt) REVERT: C 57 THR cc_start: 0.8175 (p) cc_final: 0.7836 (t) REVERT: C 68 THR cc_start: 0.8565 (p) cc_final: 0.8323 (t) REVERT: C 75 LYS cc_start: 0.8446 (ptmt) cc_final: 0.8230 (ptpp) REVERT: C 77 GLN cc_start: 0.8368 (pt0) cc_final: 0.8144 (pt0) outliers start: 45 outliers final: 37 residues processed: 277 average time/residue: 0.1627 time to fit residues: 60.5818 Evaluate side-chains 287 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 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 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 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 194 CYS 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 110 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 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 67 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.0770 chunk 96 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.2538 ------------------------------------------------------------------------------- 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 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8920 Z= 0.169 Angle : 0.675 20.760 12149 Z= 0.331 Chirality : 0.047 0.305 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.907 56.321 1238 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.05 % Favored : 89.86 % Rotamer: Outliers : 4.49 % Allowed : 20.63 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.23), residues: 1114 helix: -3.50 (0.78), residues: 30 sheet: -1.46 (0.29), residues: 293 loop : -2.29 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 34 HIS 0.003 0.000 HIS B 198 PHE 0.021 0.001 PHE A 497 TYR 0.027 0.001 TYR C 50 ARG 0.006 0.001 ARG C 66 *********************** 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 297 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7152 (mm) REVERT: A 60 PHE cc_start: 0.6837 (m-80) cc_final: 0.6478 (m-80) REVERT: A 82 ASN cc_start: 0.7049 (m-40) cc_final: 0.6582 (m-40) REVERT: A 236 THR cc_start: 0.7807 (m) cc_final: 0.7317 (t) REVERT: A 246 ARG cc_start: 0.7342 (mtm110) cc_final: 0.6526 (ptm-80) REVERT: A 269 TYR cc_start: 0.6685 (m-80) cc_final: 0.6281 (m-10) REVERT: A 355 ARG cc_start: 0.7300 (ttt180) cc_final: 0.6770 (ttt180) REVERT: A 360 ASN cc_start: 0.7818 (m-40) cc_final: 0.7572 (m-40) REVERT: A 364 ASP cc_start: 0.6980 (t70) cc_final: 0.6652 (t0) REVERT: A 378 LYS cc_start: 0.7237 (pttm) cc_final: 0.7027 (pttm) REVERT: A 396 TYR cc_start: 0.8370 (m-80) cc_final: 0.7829 (m-10) REVERT: A 434 ILE cc_start: 0.8280 (mp) cc_final: 0.7990 (mt) REVERT: A 509 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6627 (mmt90) REVERT: A 523 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7356 (p) REVERT: A 556 ASN cc_start: 0.7668 (m-40) cc_final: 0.7464 (m-40) REVERT: A 586 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6733 (m-30) REVERT: A 587 ILE cc_start: 0.8784 (mt) cc_final: 0.8553 (mt) REVERT: A 612 TYR cc_start: 0.7318 (m-80) cc_final: 0.6238 (m-80) REVERT: A 627 ASP cc_start: 0.5468 (p0) cc_final: 0.5158 (p0) REVERT: A 629 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7140 (mt) REVERT: A 656 VAL cc_start: 0.7013 (t) cc_final: 0.6772 (p) REVERT: B 9 SER cc_start: 0.7785 (m) cc_final: 0.7511 (p) REVERT: B 42 LYS cc_start: 0.7991 (mtmp) cc_final: 0.7717 (mtmp) REVERT: B 108 ARG cc_start: 0.7117 (mmt90) cc_final: 0.6795 (mmt90) REVERT: B 147 GLN cc_start: 0.6527 (tm-30) cc_final: 0.6175 (tm-30) REVERT: B 179 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6681 (tm) REVERT: B 181 LEU cc_start: 0.8354 (mt) cc_final: 0.8015 (tp) REVERT: C 35 THR cc_start: 0.7546 (p) cc_final: 0.7090 (p) REVERT: C 45 LEU cc_start: 0.8540 (mm) cc_final: 0.8282 (mt) REVERT: C 57 THR cc_start: 0.8135 (p) cc_final: 0.7846 (t) REVERT: C 68 THR cc_start: 0.8550 (p) cc_final: 0.8299 (t) REVERT: C 75 LYS cc_start: 0.8333 (ptmt) cc_final: 0.8083 (ptpp) REVERT: C 77 GLN cc_start: 0.8349 (pt0) cc_final: 0.8147 (pt0) outliers start: 44 outliers final: 36 residues processed: 275 average time/residue: 0.2035 time to fit residues: 74.1480 Evaluate side-chains 287 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG 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 629 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 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 98 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.0170 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8920 Z= 0.190 Angle : 0.688 19.763 12149 Z= 0.340 Chirality : 0.048 0.306 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.901 54.666 1238 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.34 % Favored : 90.57 % Rotamer: Outliers : 4.49 % Allowed : 20.53 % Favored : 74.97 % 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: -2.98 (0.24), residues: 1114 helix: -3.47 (0.69), residues: 30 sheet: -1.34 (0.29), residues: 308 loop : -2.34 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 34 HIS 0.003 0.000 HIS B 198 PHE 0.020 0.001 PHE A 497 TYR 0.024 0.001 TYR C 50 ARG 0.006 0.001 ARG C 66 *********************** 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 289 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 60 PHE cc_start: 0.6807 (m-80) cc_final: 0.6488 (m-80) REVERT: A 82 ASN cc_start: 0.7121 (m-40) cc_final: 0.6624 (m-40) REVERT: A 360 ASN cc_start: 0.7867 (m-40) cc_final: 0.7620 (m-40) REVERT: A 364 ASP cc_start: 0.6925 (t70) cc_final: 0.6598 (t0) REVERT: A 434 ILE cc_start: 0.8282 (mp) cc_final: 0.7972 (mt) REVERT: A 454 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6955 (ttp80) REVERT: A 509 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6646 (mmt90) REVERT: A 523 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7383 (p) REVERT: A 540 ASN cc_start: 0.5461 (m-40) cc_final: 0.5180 (m-40) REVERT: A 565 PHE cc_start: 0.6432 (t80) cc_final: 0.6206 (t80) REVERT: A 578 ASP cc_start: 0.7318 (m-30) cc_final: 0.7079 (m-30) REVERT: A 586 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: A 587 ILE cc_start: 0.8780 (mt) cc_final: 0.8561 (mt) REVERT: A 612 TYR cc_start: 0.7360 (m-80) cc_final: 0.6276 (m-80) REVERT: A 627 ASP cc_start: 0.5515 (p0) cc_final: 0.5154 (p0) REVERT: A 629 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7103 (mt) REVERT: A 656 VAL cc_start: 0.6983 (t) cc_final: 0.6739 (p) REVERT: B 9 SER cc_start: 0.7799 (m) cc_final: 0.7505 (p) REVERT: B 42 LYS cc_start: 0.7981 (mtmp) cc_final: 0.7706 (mtmp) REVERT: B 108 ARG cc_start: 0.7122 (mmt90) cc_final: 0.6791 (mmt90) REVERT: B 179 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6683 (tm) REVERT: B 181 LEU cc_start: 0.8369 (mt) cc_final: 0.8052 (tp) REVERT: C 35 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7335 (p) REVERT: C 45 LEU cc_start: 0.8613 (mm) cc_final: 0.8292 (mt) REVERT: C 57 THR cc_start: 0.8156 (p) cc_final: 0.7912 (t) REVERT: C 68 THR cc_start: 0.8609 (p) cc_final: 0.8334 (t) REVERT: C 77 GLN cc_start: 0.8387 (pt0) cc_final: 0.8171 (pt0) outliers start: 44 outliers final: 34 residues processed: 268 average time/residue: 0.2521 time to fit residues: 91.2943 Evaluate side-chains 281 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 319 ARG 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 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 C residue 11 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 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 49 optimal weight: 2.9990 chunk 72 optimal weight: 0.0270 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.0020 chunk 26 optimal weight: 0.8980 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8920 Z= 0.173 Angle : 0.691 20.307 12149 Z= 0.339 Chirality : 0.048 0.296 1355 Planarity : 0.005 0.061 1563 Dihedral : 5.777 54.200 1237 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.52 % Favored : 90.39 % Rotamer: Outliers : 4.09 % Allowed : 20.84 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.24), residues: 1114 helix: -3.40 (0.71), residues: 30 sheet: -1.24 (0.29), residues: 308 loop : -2.27 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 34 HIS 0.003 0.000 HIS B 198 PHE 0.020 0.001 PHE A 497 TYR 0.024 0.001 TYR C 50 ARG 0.007 0.001 ARG C 66 ********************** 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 283 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.6159 (t0) cc_final: 0.5863 (m-30) REVERT: A 57 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7297 (mm) REVERT: A 60 PHE cc_start: 0.6718 (m-80) cc_final: 0.6408 (m-80) REVERT: A 82 ASN cc_start: 0.7123 (m-40) cc_final: 0.6631 (m-40) REVERT: A 236 THR cc_start: 0.7721 (m) cc_final: 0.7234 (t) REVERT: A 355 ARG cc_start: 0.7309 (ttt180) cc_final: 0.6797 (ttt180) REVERT: A 364 ASP cc_start: 0.6847 (t70) cc_final: 0.6545 (t0) REVERT: A 396 TYR cc_start: 0.8342 (m-80) cc_final: 0.7783 (m-10) REVERT: A 434 ILE cc_start: 0.8237 (mp) cc_final: 0.7921 (mt) REVERT: A 454 ARG cc_start: 0.7143 (tpp80) cc_final: 0.6898 (ttp80) REVERT: A 489 TYR cc_start: 0.6785 (m-80) cc_final: 0.6492 (m-10) REVERT: A 501 TYR cc_start: 0.7612 (m-80) cc_final: 0.7259 (m-80) REVERT: A 509 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6642 (mmt90) REVERT: A 523 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7365 (p) REVERT: A 565 PHE cc_start: 0.6435 (t80) cc_final: 0.6212 (t80) REVERT: A 586 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: A 612 TYR cc_start: 0.7330 (m-80) cc_final: 0.6255 (m-80) REVERT: A 627 ASP cc_start: 0.5422 (p0) cc_final: 0.5040 (p0) REVERT: A 629 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7067 (mp) REVERT: A 656 VAL cc_start: 0.6989 (t) cc_final: 0.6740 (p) REVERT: B 9 SER cc_start: 0.7784 (m) cc_final: 0.7499 (p) REVERT: B 42 LYS cc_start: 0.7916 (mtmp) cc_final: 0.7642 (mtmp) REVERT: B 97 THR cc_start: 0.8626 (t) cc_final: 0.8280 (p) REVERT: B 108 ARG cc_start: 0.7160 (mmt90) cc_final: 0.6871 (mmt90) REVERT: B 179 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6674 (tm) REVERT: B 181 LEU cc_start: 0.8426 (mt) cc_final: 0.8106 (tp) REVERT: C 11 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7051 (tp) REVERT: C 35 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7309 (p) REVERT: C 45 LEU cc_start: 0.8579 (mm) cc_final: 0.8268 (mt) REVERT: C 68 THR cc_start: 0.8641 (p) cc_final: 0.8344 (t) REVERT: C 77 GLN cc_start: 0.8367 (pt0) cc_final: 0.8161 (pt0) outliers start: 40 outliers final: 29 residues processed: 263 average time/residue: 0.2383 time to fit residues: 83.9444 Evaluate side-chains 280 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 244 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 ARG 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 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 177 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 47 TRP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 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 80 optimal weight: 0.8980 chunk 12 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.0570 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN B 38 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.193696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.161292 restraints weight = 15516.593| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.97 r_work: 0.3925 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8920 Z= 0.229 Angle : 0.724 18.555 12149 Z= 0.359 Chirality : 0.049 0.305 1355 Planarity : 0.005 0.062 1563 Dihedral : 5.973 54.591 1237 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.59 % Favored : 89.23 % Rotamer: Outliers : 3.88 % Allowed : 21.45 % Favored : 74.67 % 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: -2.93 (0.24), residues: 1114 helix: -3.64 (0.56), residues: 41 sheet: -1.30 (0.29), residues: 316 loop : -2.26 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 34 HIS 0.003 0.000 HIS A 70 PHE 0.021 0.001 PHE A 497 TYR 0.025 0.001 TYR C 50 ARG 0.007 0.001 ARG A 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.59 seconds wall clock time: 54 minutes 23.16 seconds (3263.16 seconds total)