Starting phenix.real_space_refine on Sun May 11 08:15:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kek_37161/05_2025/8kek_37161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kek_37161/05_2025/8kek_37161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kek_37161/05_2025/8kek_37161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kek_37161/05_2025/8kek_37161.map" model { file = "/net/cci-nas-00/data/ceres_data/8kek_37161/05_2025/8kek_37161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kek_37161/05_2025/8kek_37161.cif" } resolution = 3.54 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= 0.001 sd= 0.021 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 32 5.16 5 C 4921 2.51 5 N 1285 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7721 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "A" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4460 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 32, 'TRANS': 532} Chain breaks: 4 Time building chain proxies: 4.71, per 1000 atoms: 0.61 Number of scatterers: 7721 At special positions: 0 Unit cell: (88.06, 117.81, 127.33, 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 32 16.00 O 1483 8.00 N 1285 7.00 C 4921 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 19 sheets defined 5.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.580A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.667A pdb=" N GLY A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.545A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.538A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.809A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 605 through 612 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.740A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER H 77 " --> pdb=" O GLU H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.547A pdb=" N ILE H 34 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H 91 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'H' and resid 202 through 203 removed outlier: 3.944A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.729A pdb=" N GLU L 106 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 21 through 22 removed outlier: 4.314A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.104A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.920A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.783A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 198 " --> pdb=" O LYS L 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.705A pdb=" N TYR A 53 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.912A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 87 through 91 removed outlier: 4.010A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 187 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 197 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.276A pdb=" N ILE A 117 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 124 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 119 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 163 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.643A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 300 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 583 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 595 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 312 through 313 removed outlier: 3.623A pdb=" N GLY A 536 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.018A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 386 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 500 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.518A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.629A pdb=" N TYR A 440 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 479 " --> pdb=" O TYR A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 551 through 553 137 hydrogen bonds defined for protein. 345 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: 2.20 Time building geometry restraints manager: 2.35 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: 2454 1.34 - 1.46: 1907 1.46 - 1.58: 3515 1.58 - 1.70: 0 1.70 - 1.81: 40 Bond restraints: 7916 Sorted by residual: bond pdb=" N ASN A 129 " pdb=" CA ASN A 129 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.22e-02 6.72e+03 7.11e+00 bond pdb=" N CYS A 128 " pdb=" CA CYS A 128 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.27e-02 6.20e+03 4.88e+00 bond pdb=" N PHE A 130 " pdb=" CA PHE A 130 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.50e-02 4.44e+03 4.25e+00 bond pdb=" N GLU A 131 " pdb=" CA GLU A 131 " ideal model delta sigma weight residual 1.461 1.487 -0.026 1.51e-02 4.39e+03 2.95e+00 bond pdb=" N LEU A 132 " pdb=" CA LEU A 132 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.63e+00 ... (remaining 7911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10615 1.67 - 3.33: 136 3.33 - 5.00: 17 5.00 - 6.67: 5 6.67 - 8.33: 1 Bond angle restraints: 10774 Sorted by residual: angle pdb=" N CYS A 128 " pdb=" CA CYS A 128 " pdb=" C CYS A 128 " ideal model delta sigma weight residual 114.75 110.93 3.82 1.26e+00 6.30e-01 9.17e+00 angle pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" O ASN A 129 " ideal model delta sigma weight residual 121.16 118.30 2.86 1.12e+00 7.97e-01 6.53e+00 angle pdb=" CA GLU A 131 " pdb=" C GLU A 131 " pdb=" O GLU A 131 " ideal model delta sigma weight residual 121.94 117.86 4.08 1.68e+00 3.54e-01 5.89e+00 angle pdb=" CA PHE A 130 " pdb=" C PHE A 130 " pdb=" O PHE A 130 " ideal model delta sigma weight residual 121.60 118.80 2.80 1.21e+00 6.83e-01 5.36e+00 angle pdb=" N ASP H 110 " pdb=" CA ASP H 110 " pdb=" C ASP H 110 " ideal model delta sigma weight residual 111.02 113.73 -2.71 1.22e+00 6.72e-01 4.92e+00 ... (remaining 10769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 4453 15.61 - 31.22: 169 31.22 - 46.83: 55 46.83 - 62.44: 11 62.44 - 78.05: 1 Dihedral angle restraints: 4689 sinusoidal: 1808 harmonic: 2881 Sorted by residual: dihedral pdb=" CA ASN H 104 " pdb=" C ASN H 104 " pdb=" N ILE H 105 " pdb=" CA ILE H 105 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA MET H 109 " pdb=" C MET H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA THR A 468 " pdb=" C THR A 468 " pdb=" N PRO A 469 " pdb=" CA PRO A 469 " ideal model delta harmonic sigma weight residual 180.00 -163.66 -16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 703 0.028 - 0.056: 306 0.056 - 0.084: 95 0.084 - 0.112: 87 0.112 - 0.140: 11 Chirality restraints: 1202 Sorted by residual: chirality pdb=" CA LEU A 132 " pdb=" N LEU A 132 " pdb=" C LEU A 132 " pdb=" CB LEU A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1199 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 94 " 0.026 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO L 95 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 574 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 575 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 575 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 575 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 308 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.05e+00 pdb=" N PRO A 309 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.014 5.00e-02 4.00e+02 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1232 2.77 - 3.30: 7144 3.30 - 3.84: 12179 3.84 - 4.37: 13612 4.37 - 4.90: 23788 Nonbonded interactions: 57955 Sorted by model distance: nonbonded pdb=" O PHE A 103 " pdb=" OG SER A 113 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR H 108 " pdb=" OG1 THR L 53 " model vdw 2.241 3.040 nonbonded pdb=" O TYR L 187 " pdb=" OH TYR L 193 " model vdw 2.267 3.040 nonbonded pdb=" O GLY A 326 " pdb=" ND2 ASN A 330 " model vdw 2.294 3.120 nonbonded pdb=" ND2 ASN H 162 " pdb=" O THR H 200 " model vdw 2.303 3.120 ... (remaining 57950 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 group one per residue 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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.580 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 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 0.051 7927 Z= 0.107 Angle : 0.490 8.333 10796 Z= 0.265 Chirality : 0.042 0.140 1202 Planarity : 0.003 0.038 1385 Dihedral : 9.406 78.054 2814 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.92 % Favored : 88.98 % Rotamer: Outliers : 6.01 % Allowed : 6.94 % Favored : 87.05 % 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: -5.10 (0.21), residues: 980 helix: -2.59 (0.70), residues: 35 sheet: -2.68 (0.30), residues: 248 loop : -4.02 (0.18), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.004 0.000 HIS H 35 PHE 0.007 0.001 PHE A 360 TYR 0.004 0.001 TYR H 108 ARG 0.001 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.29211 ( 137) hydrogen bonds : angle 12.08951 ( 345) SS BOND : bond 0.00122 ( 11) SS BOND : angle 0.48191 ( 22) covalent geometry : bond 0.00209 ( 7916) covalent geometry : angle 0.48976 (10774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.8101 (tt) cc_final: 0.7042 (tt) REVERT: H 20 LEU cc_start: 0.8070 (mp) cc_final: 0.7517 (mt) REVERT: H 59 TYR cc_start: 0.7323 (m-80) cc_final: 0.6990 (m-80) REVERT: H 75 LYS cc_start: 0.7102 (ttmt) cc_final: 0.6864 (ttmt) REVERT: H 106 TYR cc_start: 0.4608 (OUTLIER) cc_final: 0.4240 (p90) REVERT: L 12 SER cc_start: 0.8441 (t) cc_final: 0.8101 (p) REVERT: L 46 LEU cc_start: 0.4699 (OUTLIER) cc_final: 0.4464 (tt) REVERT: L 76 SER cc_start: 0.7466 (m) cc_final: 0.7101 (p) REVERT: L 99 PHE cc_start: 0.6806 (m-80) cc_final: 0.6452 (m-80) REVERT: L 143 ARG cc_start: 0.7074 (tmm160) cc_final: 0.6807 (tmt170) REVERT: L 172 SER cc_start: 0.7316 (m) cc_final: 0.6995 (t) REVERT: A 37 MET cc_start: 0.5258 (mtm) cc_final: 0.4980 (mmt) REVERT: A 53 TYR cc_start: 0.7113 (t80) cc_final: 0.6752 (t80) REVERT: A 65 ASN cc_start: 0.7970 (t0) cc_final: 0.7597 (p0) REVERT: A 78 ASN cc_start: -0.2897 (OUTLIER) cc_final: -0.4910 (t0) REVERT: A 260 THR cc_start: 0.7732 (p) cc_final: 0.7348 (p) REVERT: A 360 PHE cc_start: 0.7345 (p90) cc_final: 0.7111 (p90) REVERT: A 370 SER cc_start: 0.8497 (m) cc_final: 0.8161 (t) REVERT: A 383 TYR cc_start: 0.7690 (m-80) cc_final: 0.7464 (m-80) REVERT: A 389 VAL cc_start: 0.7627 (OUTLIER) cc_final: 0.7361 (t) REVERT: A 416 PHE cc_start: 0.6994 (t80) cc_final: 0.6713 (t80) REVERT: A 424 ASN cc_start: 0.8203 (t0) cc_final: 0.7963 (t0) REVERT: A 454 ASP cc_start: 0.7382 (t70) cc_final: 0.7005 (t0) REVERT: A 500 SER cc_start: 0.8071 (m) cc_final: 0.7704 (t) REVERT: A 545 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6197 (t80) outliers start: 52 outliers final: 17 residues processed: 234 average time/residue: 0.2161 time to fit residues: 65.7909 Evaluate side-chains 194 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN H 81 GLN H 104 ASN H 171 HIS H 178 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 101 GLN L 156 GLN A 33 HIS A 70 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 427 ASN A 530 ASN A 550 GLN A 632 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.212431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.187270 restraints weight = 14154.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.191719 restraints weight = 7701.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.194583 restraints weight = 4898.245| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5692 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7927 Z= 0.142 Angle : 0.622 9.665 10796 Z= 0.317 Chirality : 0.046 0.173 1202 Planarity : 0.005 0.042 1385 Dihedral : 6.876 59.170 1120 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.06 % Favored : 86.84 % Rotamer: Outliers : 5.20 % Allowed : 13.06 % Favored : 81.73 % 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: -4.44 (0.23), residues: 980 helix: -2.06 (0.82), residues: 35 sheet: -1.90 (0.31), residues: 255 loop : -3.70 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 101 HIS 0.007 0.001 HIS A 70 PHE 0.035 0.002 PHE H 29 TYR 0.013 0.001 TYR H 59 ARG 0.006 0.001 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 137) hydrogen bonds : angle 7.86636 ( 345) SS BOND : bond 0.00309 ( 11) SS BOND : angle 2.02631 ( 22) covalent geometry : bond 0.00340 ( 7916) covalent geometry : angle 0.61573 (10774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8068 (t) cc_final: 0.7746 (p) REVERT: H 18 LEU cc_start: 0.7637 (tt) cc_final: 0.7042 (tp) REVERT: H 82 MET cc_start: 0.7053 (mtm) cc_final: 0.6746 (mpp) REVERT: H 104 ASN cc_start: 0.6538 (OUTLIER) cc_final: 0.6314 (p0) REVERT: H 106 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4129 (p90) REVERT: L 12 SER cc_start: 0.8671 (t) cc_final: 0.8395 (p) REVERT: L 75 ILE cc_start: 0.8275 (mt) cc_final: 0.8056 (mt) REVERT: L 92 TYR cc_start: 0.7921 (t80) cc_final: 0.7501 (t80) REVERT: L 99 PHE cc_start: 0.6722 (m-80) cc_final: 0.6429 (m-80) REVERT: L 143 ARG cc_start: 0.7179 (tmm160) cc_final: 0.6915 (tmt170) REVERT: L 172 SER cc_start: 0.7177 (m) cc_final: 0.6825 (t) REVERT: A 53 TYR cc_start: 0.7134 (t80) cc_final: 0.6617 (t80) REVERT: A 65 ASN cc_start: 0.7839 (t0) cc_final: 0.7588 (p0) REVERT: A 78 ASN cc_start: -0.2102 (OUTLIER) cc_final: -0.4469 (t0) REVERT: A 99 ARG cc_start: 0.5821 (ptm160) cc_final: 0.5606 (ptm160) REVERT: A 260 THR cc_start: 0.7895 (p) cc_final: 0.7535 (p) REVERT: A 353 SER cc_start: 0.8621 (m) cc_final: 0.8135 (t) REVERT: A 370 SER cc_start: 0.8422 (m) cc_final: 0.8054 (p) REVERT: A 389 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7681 (t) REVERT: A 412 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7524 (mp) REVERT: A 416 PHE cc_start: 0.7191 (t80) cc_final: 0.6704 (t80) REVERT: A 424 ASN cc_start: 0.8121 (t0) cc_final: 0.7893 (t0) REVERT: A 454 ASP cc_start: 0.7666 (t70) cc_final: 0.7348 (t0) REVERT: A 545 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6297 (t80) outliers start: 45 outliers final: 26 residues processed: 204 average time/residue: 0.2107 time to fit residues: 56.5072 Evaluate side-chains 193 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.0070 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 104 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN A 129 ASN A 230 ASN A 530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.210466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185126 restraints weight = 14168.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.189724 restraints weight = 7616.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.192724 restraints weight = 4775.278| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5711 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 7927 Z= 0.125 Angle : 0.604 8.891 10796 Z= 0.307 Chirality : 0.045 0.189 1202 Planarity : 0.004 0.042 1385 Dihedral : 6.728 60.728 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.55 % Favored : 87.35 % Rotamer: Outliers : 5.55 % Allowed : 14.10 % Favored : 80.35 % 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: -4.09 (0.24), residues: 980 helix: -2.35 (0.74), residues: 41 sheet: -1.44 (0.33), residues: 256 loop : -3.53 (0.20), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 112 HIS 0.002 0.000 HIS A 149 PHE 0.035 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.003 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 137) hydrogen bonds : angle 6.93721 ( 345) SS BOND : bond 0.00451 ( 11) SS BOND : angle 1.97946 ( 22) covalent geometry : bond 0.00303 ( 7916) covalent geometry : angle 0.59782 (10774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8019 (t) cc_final: 0.7780 (p) REVERT: H 18 LEU cc_start: 0.7610 (tt) cc_final: 0.6995 (tp) REVERT: H 82 MET cc_start: 0.7277 (mtm) cc_final: 0.7016 (mpp) REVERT: H 106 TYR cc_start: 0.4510 (OUTLIER) cc_final: 0.4196 (p90) REVERT: L 12 SER cc_start: 0.8785 (t) cc_final: 0.8456 (p) REVERT: L 76 SER cc_start: 0.7527 (m) cc_final: 0.7156 (p) REVERT: L 92 TYR cc_start: 0.7909 (t80) cc_final: 0.7479 (t80) REVERT: L 99 PHE cc_start: 0.6751 (m-80) cc_final: 0.6414 (m-80) REVERT: L 143 ARG cc_start: 0.7363 (tmm160) cc_final: 0.7094 (tpt170) REVERT: L 172 SER cc_start: 0.7102 (m) cc_final: 0.6772 (t) REVERT: A 53 TYR cc_start: 0.7310 (t80) cc_final: 0.6808 (t80) REVERT: A 65 ASN cc_start: 0.7813 (t0) cc_final: 0.7502 (p0) REVERT: A 78 ASN cc_start: -0.2105 (OUTLIER) cc_final: -0.4564 (t0) REVERT: A 99 ARG cc_start: 0.5795 (ptm160) cc_final: 0.5576 (ptm160) REVERT: A 260 THR cc_start: 0.7825 (p) cc_final: 0.7482 (p) REVERT: A 306 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6353 (mtm-85) REVERT: A 353 SER cc_start: 0.8634 (m) cc_final: 0.8127 (p) REVERT: A 370 SER cc_start: 0.8398 (m) cc_final: 0.8009 (p) REVERT: A 389 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.6035 (t) REVERT: A 416 PHE cc_start: 0.7263 (t80) cc_final: 0.6913 (t80) REVERT: A 424 ASN cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: A 454 ASP cc_start: 0.7676 (t70) cc_final: 0.7309 (t0) REVERT: A 530 ASN cc_start: 0.6331 (OUTLIER) cc_final: 0.5988 (m110) REVERT: A 537 VAL cc_start: 0.7805 (m) cc_final: 0.7456 (p) REVERT: A 545 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6347 (t80) outliers start: 48 outliers final: 29 residues processed: 196 average time/residue: 0.2030 time to fit residues: 53.5153 Evaluate side-chains 188 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.0020 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 80 optimal weight: 0.1980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.208181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.182839 restraints weight = 13953.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.187363 restraints weight = 7517.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.190371 restraints weight = 4733.881| |-----------------------------------------------------------------------------| r_work (final): 0.4390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7927 Z= 0.134 Angle : 0.602 8.510 10796 Z= 0.307 Chirality : 0.045 0.158 1202 Planarity : 0.004 0.048 1385 Dihedral : 6.968 66.360 1114 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.37 % Favored : 86.53 % Rotamer: Outliers : 5.90 % Allowed : 15.03 % Favored : 79.08 % 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: -3.91 (0.24), residues: 980 helix: -1.99 (0.76), residues: 41 sheet: -1.28 (0.32), residues: 261 loop : -3.45 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 340 HIS 0.002 0.000 HIS A 149 PHE 0.024 0.001 PHE H 29 TYR 0.013 0.001 TYR H 94 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02798 ( 137) hydrogen bonds : angle 6.45228 ( 345) SS BOND : bond 0.00381 ( 11) SS BOND : angle 1.59887 ( 22) covalent geometry : bond 0.00319 ( 7916) covalent geometry : angle 0.59875 (10774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.7639 (tt) cc_final: 0.7002 (tp) REVERT: H 82 MET cc_start: 0.7302 (mtm) cc_final: 0.7024 (mpp) REVERT: H 106 TYR cc_start: 0.4561 (OUTLIER) cc_final: 0.4153 (p90) REVERT: L 12 SER cc_start: 0.8725 (t) cc_final: 0.8382 (p) REVERT: L 92 TYR cc_start: 0.7894 (t80) cc_final: 0.7490 (t80) REVERT: L 99 PHE cc_start: 0.6746 (m-80) cc_final: 0.6413 (m-80) REVERT: L 143 ARG cc_start: 0.7408 (tmm160) cc_final: 0.7041 (tpt170) REVERT: L 166 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7331 (tm-30) REVERT: L 172 SER cc_start: 0.7117 (m) cc_final: 0.6781 (t) REVERT: A 53 TYR cc_start: 0.7280 (t80) cc_final: 0.6688 (t80) REVERT: A 65 ASN cc_start: 0.7694 (t0) cc_final: 0.7398 (p0) REVERT: A 78 ASN cc_start: -0.1690 (OUTLIER) cc_final: -0.4156 (t0) REVERT: A 200 TYR cc_start: 0.6930 (m-80) cc_final: 0.6443 (m-80) REVERT: A 201 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7184 (tm-30) REVERT: A 260 THR cc_start: 0.7773 (p) cc_final: 0.7428 (p) REVERT: A 306 ARG cc_start: 0.7183 (mtm-85) cc_final: 0.6256 (mtm-85) REVERT: A 353 SER cc_start: 0.8717 (m) cc_final: 0.8195 (p) REVERT: A 357 ASN cc_start: 0.7888 (t0) cc_final: 0.7478 (t0) REVERT: A 370 SER cc_start: 0.8312 (m) cc_final: 0.7940 (p) REVERT: A 412 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7619 (mp) REVERT: A 416 PHE cc_start: 0.7203 (t80) cc_final: 0.6900 (t80) REVERT: A 424 ASN cc_start: 0.8169 (t0) cc_final: 0.7896 (t0) REVERT: A 454 ASP cc_start: 0.7648 (t70) cc_final: 0.7281 (t0) REVERT: A 537 VAL cc_start: 0.7829 (m) cc_final: 0.7513 (p) REVERT: A 545 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6522 (t80) outliers start: 51 outliers final: 24 residues processed: 198 average time/residue: 0.1982 time to fit residues: 52.3863 Evaluate side-chains 180 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 0.0670 chunk 96 optimal weight: 0.0870 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.206494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.181389 restraints weight = 13922.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.185870 restraints weight = 7576.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188818 restraints weight = 4767.086| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5787 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7927 Z= 0.140 Angle : 0.612 9.338 10796 Z= 0.310 Chirality : 0.046 0.201 1202 Planarity : 0.004 0.045 1385 Dihedral : 6.837 69.262 1108 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.47 % Favored : 86.43 % Rotamer: Outliers : 4.97 % Allowed : 16.65 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -3.73 (0.24), residues: 980 helix: -0.85 (0.92), residues: 35 sheet: -1.14 (0.33), residues: 251 loop : -3.36 (0.20), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 340 HIS 0.002 0.000 HIS A 149 PHE 0.025 0.001 PHE H 153 TYR 0.013 0.001 TYR H 94 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02695 ( 137) hydrogen bonds : angle 6.22177 ( 345) SS BOND : bond 0.00371 ( 11) SS BOND : angle 1.68227 ( 22) covalent geometry : bond 0.00330 ( 7916) covalent geometry : angle 0.60792 (10774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6969 (tt) REVERT: H 82 MET cc_start: 0.7390 (mtm) cc_final: 0.7058 (mpp) REVERT: H 106 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4135 (p90) REVERT: L 12 SER cc_start: 0.8706 (t) cc_final: 0.8341 (p) REVERT: L 76 SER cc_start: 0.7488 (m) cc_final: 0.7178 (p) REVERT: L 99 PHE cc_start: 0.6737 (m-80) cc_final: 0.6355 (m-80) REVERT: L 143 ARG cc_start: 0.7513 (tmm160) cc_final: 0.6983 (tpt170) REVERT: L 172 SER cc_start: 0.7113 (m) cc_final: 0.6755 (t) REVERT: A 65 ASN cc_start: 0.7627 (t0) cc_final: 0.7358 (p0) REVERT: A 78 ASN cc_start: -0.1662 (OUTLIER) cc_final: -0.4012 (t0) REVERT: A 200 TYR cc_start: 0.6937 (m-80) cc_final: 0.6438 (m-80) REVERT: A 201 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 260 THR cc_start: 0.7782 (p) cc_final: 0.7501 (p) REVERT: A 306 ARG cc_start: 0.7210 (mtm-85) cc_final: 0.6341 (mtm-85) REVERT: A 353 SER cc_start: 0.8766 (m) cc_final: 0.8296 (p) REVERT: A 357 ASN cc_start: 0.7871 (t0) cc_final: 0.7499 (t0) REVERT: A 370 SER cc_start: 0.8370 (m) cc_final: 0.7990 (p) REVERT: A 393 ASP cc_start: 0.6413 (p0) cc_final: 0.6191 (p0) REVERT: A 395 ARG cc_start: 0.6808 (mtm110) cc_final: 0.6491 (mtm180) REVERT: A 416 PHE cc_start: 0.7302 (t80) cc_final: 0.7091 (t80) REVERT: A 454 ASP cc_start: 0.7618 (t70) cc_final: 0.7240 (t0) REVERT: A 465 LYS cc_start: 0.8462 (tppt) cc_final: 0.8127 (tppt) REVERT: A 537 VAL cc_start: 0.7851 (m) cc_final: 0.7539 (p) REVERT: A 545 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6470 (t80) outliers start: 43 outliers final: 26 residues processed: 192 average time/residue: 0.2050 time to fit residues: 52.2637 Evaluate side-chains 184 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN L 125 GLN A 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.207777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.182772 restraints weight = 13795.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.187296 restraints weight = 7390.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.190329 restraints weight = 4631.010| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5760 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7927 Z= 0.113 Angle : 0.597 10.122 10796 Z= 0.297 Chirality : 0.045 0.177 1202 Planarity : 0.004 0.045 1385 Dihedral : 6.739 73.397 1103 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.67 % Favored : 86.22 % Rotamer: Outliers : 4.28 % Allowed : 17.92 % Favored : 77.80 % 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: -3.52 (0.25), residues: 980 helix: -0.91 (0.93), residues: 36 sheet: -1.07 (0.34), residues: 253 loop : -3.18 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 97 HIS 0.002 0.000 HIS A 149 PHE 0.024 0.001 PHE H 29 TYR 0.012 0.001 TYR A 481 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02501 ( 137) hydrogen bonds : angle 5.94561 ( 345) SS BOND : bond 0.00233 ( 11) SS BOND : angle 0.66269 ( 22) covalent geometry : bond 0.00266 ( 7916) covalent geometry : angle 0.59690 (10774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6877 (tt) REVERT: H 82 MET cc_start: 0.7401 (mtm) cc_final: 0.7144 (mpp) REVERT: H 106 TYR cc_start: 0.4506 (OUTLIER) cc_final: 0.4118 (p90) REVERT: L 12 SER cc_start: 0.8692 (t) cc_final: 0.8330 (p) REVERT: L 31 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6836 (ptpt) REVERT: L 99 PHE cc_start: 0.6710 (m-80) cc_final: 0.6300 (m-80) REVERT: L 143 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.7005 (tpt170) REVERT: L 172 SER cc_start: 0.7068 (m) cc_final: 0.6743 (t) REVERT: A 65 ASN cc_start: 0.7723 (t0) cc_final: 0.7393 (p0) REVERT: A 78 ASN cc_start: -0.1616 (OUTLIER) cc_final: -0.4002 (t0) REVERT: A 200 TYR cc_start: 0.6999 (m-80) cc_final: 0.6478 (m-80) REVERT: A 201 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 260 THR cc_start: 0.7750 (p) cc_final: 0.7420 (p) REVERT: A 306 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6329 (mtm-85) REVERT: A 353 SER cc_start: 0.8740 (m) cc_final: 0.8262 (p) REVERT: A 357 ASN cc_start: 0.7867 (t0) cc_final: 0.7493 (t0) REVERT: A 370 SER cc_start: 0.8371 (m) cc_final: 0.7994 (p) REVERT: A 454 ASP cc_start: 0.7664 (t70) cc_final: 0.7264 (t0) REVERT: A 465 LYS cc_start: 0.8373 (tppt) cc_final: 0.8117 (tppt) REVERT: A 537 VAL cc_start: 0.7826 (m) cc_final: 0.7521 (p) REVERT: A 545 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6459 (t80) outliers start: 37 outliers final: 21 residues processed: 186 average time/residue: 0.2088 time to fit residues: 51.6979 Evaluate side-chains 180 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN A 230 ASN A 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.201947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.177472 restraints weight = 13810.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.181921 restraints weight = 7502.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.184865 restraints weight = 4702.632| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7927 Z= 0.186 Angle : 0.674 10.610 10796 Z= 0.346 Chirality : 0.047 0.186 1202 Planarity : 0.005 0.050 1385 Dihedral : 6.967 72.065 1099 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.10 % Favored : 84.80 % Rotamer: Outliers : 5.32 % Allowed : 17.34 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.25), residues: 980 helix: -0.82 (0.95), residues: 36 sheet: -0.99 (0.34), residues: 252 loop : -3.15 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.005 0.001 HIS A 149 PHE 0.025 0.002 PHE H 29 TYR 0.020 0.002 TYR H 152 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 137) hydrogen bonds : angle 6.32388 ( 345) SS BOND : bond 0.00448 ( 11) SS BOND : angle 1.17533 ( 22) covalent geometry : bond 0.00425 ( 7916) covalent geometry : angle 0.67214 (10774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7213 (tt) REVERT: H 82 MET cc_start: 0.7502 (mtm) cc_final: 0.6853 (mpp) REVERT: H 106 TYR cc_start: 0.4597 (OUTLIER) cc_final: 0.4138 (p90) REVERT: L 12 SER cc_start: 0.8659 (t) cc_final: 0.8348 (p) REVERT: L 99 PHE cc_start: 0.6803 (m-80) cc_final: 0.6385 (m-80) REVERT: L 143 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7215 (tmt-80) REVERT: L 172 SER cc_start: 0.7210 (m) cc_final: 0.6814 (t) REVERT: A 65 ASN cc_start: 0.7714 (t0) cc_final: 0.7400 (p0) REVERT: A 78 ASN cc_start: -0.1934 (OUTLIER) cc_final: -0.4190 (t0) REVERT: A 200 TYR cc_start: 0.7204 (m-80) cc_final: 0.6721 (m-80) REVERT: A 201 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 306 ARG cc_start: 0.7246 (mtm-85) cc_final: 0.6465 (mtm-85) REVERT: A 353 SER cc_start: 0.8770 (m) cc_final: 0.8350 (p) REVERT: A 357 ASN cc_start: 0.7949 (t0) cc_final: 0.7593 (t0) REVERT: A 370 SER cc_start: 0.8507 (m) cc_final: 0.7985 (p) REVERT: A 395 ARG cc_start: 0.7123 (mtm110) cc_final: 0.6842 (mtt90) REVERT: A 416 PHE cc_start: 0.7059 (t80) cc_final: 0.6498 (t80) REVERT: A 454 ASP cc_start: 0.7581 (t70) cc_final: 0.7186 (t0) REVERT: A 465 LYS cc_start: 0.8371 (tppt) cc_final: 0.8040 (tppt) REVERT: A 537 VAL cc_start: 0.7974 (m) cc_final: 0.7649 (p) REVERT: A 545 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 546 GLN cc_start: 0.6356 (tp40) cc_final: 0.6142 (tp40) outliers start: 46 outliers final: 27 residues processed: 186 average time/residue: 0.2216 time to fit residues: 54.8290 Evaluate side-chains 181 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.202723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178149 restraints weight = 13772.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182629 restraints weight = 7497.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.185608 restraints weight = 4700.899| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7927 Z= 0.143 Angle : 0.658 11.539 10796 Z= 0.331 Chirality : 0.047 0.187 1202 Planarity : 0.005 0.045 1385 Dihedral : 6.994 76.885 1099 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.98 % Favored : 85.92 % Rotamer: Outliers : 4.62 % Allowed : 18.15 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -3.31 (0.25), residues: 980 helix: -1.39 (0.87), residues: 42 sheet: -0.72 (0.35), residues: 243 loop : -3.06 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 36 HIS 0.003 0.001 HIS A 149 PHE 0.021 0.002 PHE H 29 TYR 0.014 0.001 TYR A 481 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02687 ( 137) hydrogen bonds : angle 6.17939 ( 345) SS BOND : bond 0.00464 ( 11) SS BOND : angle 1.25753 ( 22) covalent geometry : bond 0.00329 ( 7916) covalent geometry : angle 0.65644 (10774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7105 (tt) REVERT: H 82 MET cc_start: 0.7544 (mtm) cc_final: 0.7069 (mtm) REVERT: H 106 TYR cc_start: 0.4488 (OUTLIER) cc_final: 0.4053 (p90) REVERT: H 170 VAL cc_start: 0.4750 (OUTLIER) cc_final: 0.4338 (m) REVERT: L 12 SER cc_start: 0.8655 (t) cc_final: 0.8337 (p) REVERT: L 99 PHE cc_start: 0.6755 (m-80) cc_final: 0.6356 (m-80) REVERT: L 143 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7156 (tmt-80) REVERT: L 172 SER cc_start: 0.7116 (m) cc_final: 0.6752 (t) REVERT: A 65 ASN cc_start: 0.7683 (t0) cc_final: 0.7422 (p0) REVERT: A 78 ASN cc_start: -0.1726 (OUTLIER) cc_final: -0.4060 (t0) REVERT: A 200 TYR cc_start: 0.7156 (m-80) cc_final: 0.6703 (m-80) REVERT: A 201 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 306 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6933 (mtm-85) REVERT: A 348 CYS cc_start: 0.3989 (p) cc_final: 0.3279 (p) REVERT: A 353 SER cc_start: 0.8750 (m) cc_final: 0.8333 (p) REVERT: A 357 ASN cc_start: 0.7926 (t0) cc_final: 0.7585 (t0) REVERT: A 370 SER cc_start: 0.8563 (m) cc_final: 0.8047 (p) REVERT: A 416 PHE cc_start: 0.6945 (t80) cc_final: 0.6261 (t80) REVERT: A 454 ASP cc_start: 0.7454 (t70) cc_final: 0.7112 (t0) REVERT: A 537 VAL cc_start: 0.7886 (m) cc_final: 0.7548 (p) REVERT: A 545 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6580 (t80) REVERT: A 546 GLN cc_start: 0.6415 (tp40) cc_final: 0.6198 (tp-100) outliers start: 40 outliers final: 26 residues processed: 179 average time/residue: 0.1966 time to fit residues: 47.2564 Evaluate side-chains 175 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.0370 chunk 39 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 HIS A 155 ASN A 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.202374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178126 restraints weight = 13985.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.182618 restraints weight = 7568.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.185577 restraints weight = 4718.986| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7927 Z= 0.137 Angle : 0.660 11.751 10796 Z= 0.328 Chirality : 0.046 0.163 1202 Planarity : 0.005 0.047 1385 Dihedral : 6.893 80.519 1099 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.80 % Favored : 85.10 % Rotamer: Outliers : 4.05 % Allowed : 19.19 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.25), residues: 980 helix: -1.33 (0.87), residues: 42 sheet: -0.62 (0.36), residues: 245 loop : -3.02 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 36 HIS 0.003 0.001 HIS A 149 PHE 0.021 0.001 PHE H 29 TYR 0.015 0.001 TYR A 481 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02587 ( 137) hydrogen bonds : angle 6.05064 ( 345) SS BOND : bond 0.00381 ( 11) SS BOND : angle 1.11969 ( 22) covalent geometry : bond 0.00317 ( 7916) covalent geometry : angle 0.65858 (10774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7124 (tt) REVERT: H 60 LEU cc_start: 0.7903 (tt) cc_final: 0.7601 (tt) REVERT: H 82 MET cc_start: 0.7522 (mtm) cc_final: 0.6925 (mtm) REVERT: H 106 TYR cc_start: 0.4512 (OUTLIER) cc_final: 0.4119 (p90) REVERT: H 107 TYR cc_start: 0.4810 (OUTLIER) cc_final: 0.4588 (m-80) REVERT: H 170 VAL cc_start: 0.4666 (OUTLIER) cc_final: 0.4262 (m) REVERT: L 12 SER cc_start: 0.8691 (t) cc_final: 0.8341 (p) REVERT: L 31 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6940 (ptpt) REVERT: L 99 PHE cc_start: 0.6743 (m-80) cc_final: 0.6284 (m-80) REVERT: L 143 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7167 (tmt-80) REVERT: L 172 SER cc_start: 0.7117 (m) cc_final: 0.6768 (t) REVERT: A 65 ASN cc_start: 0.7853 (t0) cc_final: 0.7563 (p0) REVERT: A 78 ASN cc_start: -0.1834 (OUTLIER) cc_final: -0.4019 (t0) REVERT: A 200 TYR cc_start: 0.7188 (m-80) cc_final: 0.6733 (m-80) REVERT: A 306 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6928 (mtm-85) REVERT: A 353 SER cc_start: 0.8752 (m) cc_final: 0.8345 (p) REVERT: A 357 ASN cc_start: 0.7918 (t0) cc_final: 0.7586 (t0) REVERT: A 416 PHE cc_start: 0.6895 (t80) cc_final: 0.6208 (t80) REVERT: A 454 ASP cc_start: 0.7479 (t70) cc_final: 0.7155 (t0) REVERT: A 537 VAL cc_start: 0.7752 (m) cc_final: 0.7442 (p) REVERT: A 545 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6573 (t80) outliers start: 35 outliers final: 22 residues processed: 178 average time/residue: 0.2074 time to fit residues: 49.3804 Evaluate side-chains 176 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.203117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.178857 restraints weight = 13755.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.183355 restraints weight = 7472.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.186362 restraints weight = 4661.856| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7927 Z= 0.130 Angle : 0.678 11.975 10796 Z= 0.335 Chirality : 0.047 0.193 1202 Planarity : 0.005 0.045 1385 Dihedral : 6.867 83.313 1099 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.39 % Favored : 85.51 % Rotamer: Outliers : 3.35 % Allowed : 20.00 % Favored : 76.65 % 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: -3.14 (0.26), residues: 980 helix: -1.27 (0.86), residues: 42 sheet: -0.53 (0.36), residues: 243 loop : -2.97 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 36 HIS 0.003 0.001 HIS A 149 PHE 0.019 0.001 PHE H 29 TYR 0.019 0.001 TYR A 481 ARG 0.006 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02460 ( 137) hydrogen bonds : angle 5.98580 ( 345) SS BOND : bond 0.00333 ( 11) SS BOND : angle 1.32297 ( 22) covalent geometry : bond 0.00305 ( 7916) covalent geometry : angle 0.67610 (10774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6997 (tt) REVERT: H 60 LEU cc_start: 0.7912 (tt) cc_final: 0.7601 (tt) REVERT: H 82 MET cc_start: 0.7503 (mtm) cc_final: 0.6926 (mtm) REVERT: H 106 TYR cc_start: 0.4472 (OUTLIER) cc_final: 0.4095 (p90) REVERT: H 170 VAL cc_start: 0.4692 (OUTLIER) cc_final: 0.4319 (m) REVERT: L 11 LEU cc_start: 0.8575 (mm) cc_final: 0.8286 (mp) REVERT: L 12 SER cc_start: 0.8685 (t) cc_final: 0.8289 (p) REVERT: L 31 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6932 (ptpt) REVERT: L 99 PHE cc_start: 0.6717 (m-80) cc_final: 0.6340 (m-80) REVERT: L 143 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7110 (tmt170) REVERT: L 172 SER cc_start: 0.7066 (m) cc_final: 0.6736 (t) REVERT: A 65 ASN cc_start: 0.7851 (t0) cc_final: 0.7576 (p0) REVERT: A 78 ASN cc_start: -0.2071 (OUTLIER) cc_final: -0.4153 (t0) REVERT: A 200 TYR cc_start: 0.7128 (m-80) cc_final: 0.6714 (m-80) REVERT: A 306 ARG cc_start: 0.7195 (mtm-85) cc_final: 0.6910 (mtm-85) REVERT: A 353 SER cc_start: 0.8742 (m) cc_final: 0.8340 (p) REVERT: A 357 ASN cc_start: 0.7895 (t0) cc_final: 0.7554 (t0) REVERT: A 370 SER cc_start: 0.8511 (m) cc_final: 0.8040 (p) REVERT: A 416 PHE cc_start: 0.6879 (t80) cc_final: 0.6187 (t80) REVERT: A 454 ASP cc_start: 0.7477 (t70) cc_final: 0.7164 (t0) REVERT: A 537 VAL cc_start: 0.7784 (m) cc_final: 0.7483 (p) REVERT: A 545 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6547 (t80) outliers start: 29 outliers final: 21 residues processed: 168 average time/residue: 0.2082 time to fit residues: 46.4551 Evaluate side-chains 171 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 143 ARG Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 77 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.204386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.180349 restraints weight = 13850.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.184832 restraints weight = 7469.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.187874 restraints weight = 4661.720| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5788 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7927 Z= 0.113 Angle : 0.663 11.536 10796 Z= 0.325 Chirality : 0.046 0.178 1202 Planarity : 0.004 0.045 1385 Dihedral : 6.719 89.207 1098 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.98 % Favored : 85.92 % Rotamer: Outliers : 2.89 % Allowed : 20.58 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.26), residues: 980 helix: -1.03 (0.86), residues: 42 sheet: -0.38 (0.36), residues: 242 loop : -2.88 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 36 HIS 0.002 0.000 HIS A 149 PHE 0.017 0.001 PHE H 29 TYR 0.016 0.001 TYR A 481 ARG 0.006 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02303 ( 137) hydrogen bonds : angle 5.73217 ( 345) SS BOND : bond 0.00279 ( 11) SS BOND : angle 1.03669 ( 22) covalent geometry : bond 0.00269 ( 7916) covalent geometry : angle 0.66185 (10774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.98 seconds wall clock time: 51 minutes 53.07 seconds (3113.07 seconds total)