Starting phenix.real_space_refine on Fri Aug 22 20:37:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kek_37161/08_2025/8kek_37161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kek_37161/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8kek_37161/08_2025/8kek_37161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kek_37161/08_2025/8kek_37161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kek_37161/08_2025/8kek_37161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kek_37161/08_2025/8kek_37161.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.00, per 1000 atoms: 0.26 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: 0.60 Conformation dependent library (CDL) restraints added in 427.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.08 Time building geometry restraints manager: 0.84 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: 1.370 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.630 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.510 ------------------------------------------------------------------------------- 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 : 9.40 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG A 495 TYR 0.004 0.001 TYR H 108 PHE 0.007 0.001 PHE A 360 TRP 0.007 0.001 TRP A 423 HIS 0.004 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 7916) covalent geometry : angle 0.48976 (10774) SS BOND : bond 0.00122 ( 11) SS BOND : angle 0.48191 ( 22) hydrogen bonds : bond 0.29211 ( 137) hydrogen bonds : angle 12.08951 ( 345) *********************** 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 : 0.273 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: 0.1014 time to fit residues: 30.9602 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 : 0.223 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 427 ASN A 505 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 = 0.4669 r_free = 0.4669 target = 0.219154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.194355 restraints weight = 14291.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.198766 restraints weight = 7577.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.201682 restraints weight = 4729.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.203647 restraints weight = 3307.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.204840 restraints weight = 2537.743| |-----------------------------------------------------------------------------| r_work (final): 0.4484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7927 Z= 0.127 Angle : 0.610 9.591 10796 Z= 0.310 Chirality : 0.046 0.173 1202 Planarity : 0.004 0.042 1385 Dihedral : 6.847 59.945 1120 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.45 % Favored : 87.45 % Rotamer: Outliers : 5.32 % Allowed : 12.49 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.41 (0.23), residues: 980 helix: -2.08 (0.82), residues: 35 sheet: -1.89 (0.31), residues: 255 loop : -3.67 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 306 TYR 0.012 0.001 TYR H 59 PHE 0.031 0.002 PHE H 29 TRP 0.011 0.001 TRP A 101 HIS 0.007 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7916) covalent geometry : angle 0.60485 (10774) SS BOND : bond 0.00476 ( 11) SS BOND : angle 1.91587 ( 22) hydrogen bonds : bond 0.03844 ( 137) hydrogen bonds : angle 7.64876 ( 345) *********************** 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 218 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8040 (t) cc_final: 0.7728 (p) REVERT: H 18 LEU cc_start: 0.7590 (tt) cc_final: 0.7041 (tp) REVERT: H 82 MET cc_start: 0.7101 (mtm) cc_final: 0.6799 (mpp) REVERT: H 106 TYR cc_start: 0.4443 (OUTLIER) cc_final: 0.4088 (p90) REVERT: L 12 SER cc_start: 0.8716 (t) cc_final: 0.8484 (p) REVERT: L 92 TYR cc_start: 0.7866 (t80) cc_final: 0.7487 (t80) REVERT: L 99 PHE cc_start: 0.6752 (m-80) cc_final: 0.6470 (m-80) REVERT: L 143 ARG cc_start: 0.7227 (tmm160) cc_final: 0.6997 (tmt170) REVERT: L 172 SER cc_start: 0.7204 (m) cc_final: 0.6835 (t) REVERT: A 53 TYR cc_start: 0.7306 (t80) cc_final: 0.6772 (t80) REVERT: A 65 ASN cc_start: 0.7875 (t0) cc_final: 0.7562 (p0) REVERT: A 78 ASN cc_start: -0.2259 (OUTLIER) cc_final: -0.4510 (t0) REVERT: A 99 ARG cc_start: 0.5879 (ptm160) cc_final: 0.5643 (ptm160) REVERT: A 260 THR cc_start: 0.7884 (p) cc_final: 0.7522 (p) REVERT: A 353 SER cc_start: 0.8551 (m) cc_final: 0.8052 (t) REVERT: A 370 SER cc_start: 0.8420 (m) cc_final: 0.8024 (p) REVERT: A 389 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (t) REVERT: A 416 PHE cc_start: 0.7112 (t80) cc_final: 0.6493 (t80) REVERT: A 424 ASN cc_start: 0.8142 (t0) cc_final: 0.7928 (t0) REVERT: A 454 ASP cc_start: 0.7640 (t70) cc_final: 0.7314 (t0) REVERT: A 545 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6303 (t80) outliers start: 46 outliers final: 29 residues processed: 206 average time/residue: 0.0924 time to fit residues: 25.1330 Evaluate side-chains 191 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 166 LEU 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 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 66 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 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 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN A 70 HIS A 129 ASN A 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.209301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184131 restraints weight = 14107.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.188488 restraints weight = 7632.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.191525 restraints weight = 4838.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.193576 restraints weight = 3382.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.194898 restraints weight = 2582.166| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7927 Z= 0.140 Angle : 0.614 8.604 10796 Z= 0.314 Chirality : 0.046 0.198 1202 Planarity : 0.004 0.042 1385 Dihedral : 6.765 59.987 1114 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.76 % Favored : 87.14 % Rotamer: Outliers : 5.55 % Allowed : 14.80 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.07 (0.24), residues: 980 helix: -2.34 (0.74), residues: 41 sheet: -1.44 (0.33), residues: 256 loop : -3.52 (0.20), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 453 TYR 0.012 0.001 TYR H 94 PHE 0.034 0.001 PHE H 29 TRP 0.017 0.002 TRP H 112 HIS 0.008 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7916) covalent geometry : angle 0.60749 (10774) SS BOND : bond 0.00350 ( 11) SS BOND : angle 2.00892 ( 22) hydrogen bonds : bond 0.03155 ( 137) hydrogen bonds : angle 6.85578 ( 345) *********************** 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 207 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8066 (t) cc_final: 0.7818 (p) REVERT: H 18 LEU cc_start: 0.7646 (tt) cc_final: 0.6955 (tp) REVERT: H 48 VAL cc_start: 0.5372 (OUTLIER) cc_final: 0.5171 (p) REVERT: H 82 MET cc_start: 0.7288 (mtm) cc_final: 0.7077 (mpp) REVERT: H 106 TYR cc_start: 0.4489 (OUTLIER) cc_final: 0.4168 (p90) REVERT: L 12 SER cc_start: 0.8751 (t) cc_final: 0.8424 (p) REVERT: L 76 SER cc_start: 0.7485 (m) cc_final: 0.7218 (p) REVERT: L 92 TYR cc_start: 0.7931 (t80) cc_final: 0.7509 (t80) REVERT: L 99 PHE cc_start: 0.6715 (m-80) cc_final: 0.6391 (m-80) REVERT: L 143 ARG cc_start: 0.7364 (tmm160) cc_final: 0.7037 (tpt170) REVERT: L 172 SER cc_start: 0.7145 (m) cc_final: 0.6806 (t) REVERT: A 53 TYR cc_start: 0.7236 (t80) cc_final: 0.6744 (t80) REVERT: A 65 ASN cc_start: 0.7829 (t0) cc_final: 0.7494 (p0) REVERT: A 78 ASN cc_start: -0.2052 (OUTLIER) cc_final: -0.4486 (t0) REVERT: A 99 ARG cc_start: 0.5779 (ptm160) cc_final: 0.5565 (ptm160) REVERT: A 260 THR cc_start: 0.7850 (p) cc_final: 0.7512 (p) REVERT: A 306 ARG cc_start: 0.7173 (mtm-85) cc_final: 0.6374 (mtm-85) REVERT: A 353 SER cc_start: 0.8670 (m) cc_final: 0.8121 (p) REVERT: A 370 SER cc_start: 0.8351 (m) cc_final: 0.7982 (p) REVERT: A 383 TYR cc_start: 0.7533 (m-80) cc_final: 0.7239 (m-80) REVERT: A 389 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.6206 (t) REVERT: A 412 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 416 PHE cc_start: 0.7258 (t80) cc_final: 0.6889 (t80) REVERT: A 454 ASP cc_start: 0.7656 (t70) cc_final: 0.7298 (t0) REVERT: A 537 VAL cc_start: 0.7856 (m) cc_final: 0.7528 (p) REVERT: A 545 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6383 (t80) outliers start: 48 outliers final: 28 residues processed: 195 average time/residue: 0.0836 time to fit residues: 21.8986 Evaluate side-chains 189 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain H residue 57 THR 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 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 45 LYS 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 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 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 36 optimal weight: 0.0470 chunk 72 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 overall best weight: 0.0896 ------------------------------------------------------------------------------- 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** A 523 GLN A 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.212279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.187028 restraints weight = 14318.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.191559 restraints weight = 7736.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.194620 restraints weight = 4859.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.196639 restraints weight = 3408.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.198068 restraints weight = 2585.809| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7927 Z= 0.100 Angle : 0.568 7.814 10796 Z= 0.285 Chirality : 0.044 0.164 1202 Planarity : 0.004 0.046 1385 Dihedral : 6.687 66.932 1112 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.24 % Favored : 87.65 % Rotamer: Outliers : 5.20 % Allowed : 15.49 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.24), residues: 980 helix: -2.07 (0.75), residues: 41 sheet: -1.09 (0.33), residues: 245 loop : -3.33 (0.20), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.009 0.001 TYR A 63 PHE 0.024 0.001 PHE H 29 TRP 0.012 0.001 TRP L 97 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7916) covalent geometry : angle 0.56552 (10774) SS BOND : bond 0.00199 ( 11) SS BOND : angle 1.34861 ( 22) hydrogen bonds : bond 0.02623 ( 137) hydrogen bonds : angle 6.16032 ( 345) *********************** 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 198 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 LEU cc_start: 0.7608 (tt) cc_final: 0.6876 (tp) REVERT: H 82 MET cc_start: 0.7318 (mtm) cc_final: 0.7118 (mpp) REVERT: H 106 TYR cc_start: 0.4470 (OUTLIER) cc_final: 0.4131 (p90) REVERT: L 12 SER cc_start: 0.8743 (t) cc_final: 0.8375 (p) REVERT: L 92 TYR cc_start: 0.7810 (t80) cc_final: 0.7497 (t80) REVERT: L 99 PHE cc_start: 0.6637 (m-80) cc_final: 0.6288 (m-80) REVERT: L 172 SER cc_start: 0.6945 (m) cc_final: 0.6657 (t) REVERT: L 174 TYR cc_start: 0.6978 (m-80) cc_final: 0.6312 (m-10) REVERT: A 65 ASN cc_start: 0.7804 (t0) cc_final: 0.7387 (p0) REVERT: A 78 ASN cc_start: -0.2319 (OUTLIER) cc_final: -0.4478 (t0) REVERT: A 260 THR cc_start: 0.7810 (p) cc_final: 0.7455 (p) REVERT: A 306 ARG cc_start: 0.7085 (mtm-85) cc_final: 0.6235 (mtm-85) REVERT: A 353 SER cc_start: 0.8505 (m) cc_final: 0.8018 (t) REVERT: A 370 SER cc_start: 0.8289 (m) cc_final: 0.8084 (t) REVERT: A 416 PHE cc_start: 0.6953 (t80) cc_final: 0.6091 (t80) REVERT: A 424 ASN cc_start: 0.8258 (t0) cc_final: 0.8000 (t0) REVERT: A 454 ASP cc_start: 0.7617 (t70) cc_final: 0.7277 (t0) REVERT: A 537 VAL cc_start: 0.7644 (m) cc_final: 0.7350 (p) REVERT: A 545 PHE cc_start: 0.6835 (OUTLIER) cc_final: 0.6267 (t80) outliers start: 45 outliers final: 25 residues processed: 190 average time/residue: 0.0891 time to fit residues: 22.6999 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 : 0.240 ------------------------------------------------------------------------------- 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 75 LYS 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 119 ILE Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 72 THR 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 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 363 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 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 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 A 530 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.204595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.179756 restraints weight = 13908.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.184194 restraints weight = 7504.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.187228 restraints weight = 4728.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.189245 restraints weight = 3303.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.190722 restraints weight = 2496.876| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5717 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7927 Z= 0.164 Angle : 0.626 8.711 10796 Z= 0.321 Chirality : 0.046 0.183 1202 Planarity : 0.004 0.048 1385 Dihedral : 6.872 67.966 1109 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.88 % Favored : 86.02 % Rotamer: Outliers : 4.86 % Allowed : 15.84 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.24), residues: 980 helix: -0.92 (0.90), residues: 35 sheet: -1.12 (0.33), residues: 257 loop : -3.34 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.016 0.002 TYR H 152 PHE 0.024 0.002 PHE H 29 TRP 0.014 0.002 TRP A 340 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7916) covalent geometry : angle 0.62307 (10774) SS BOND : bond 0.00407 ( 11) SS BOND : angle 1.52137 ( 22) hydrogen bonds : bond 0.02956 ( 137) hydrogen bonds : angle 6.21921 ( 345) *********************** 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 196 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7068 (tt) REVERT: H 82 MET cc_start: 0.7476 (mtm) cc_final: 0.6950 (mpp) REVERT: H 106 TYR cc_start: 0.4567 (OUTLIER) cc_final: 0.4158 (p90) REVERT: L 11 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8104 (mp) REVERT: L 12 SER cc_start: 0.8753 (t) cc_final: 0.8384 (p) REVERT: L 76 SER cc_start: 0.7554 (m) cc_final: 0.7243 (p) REVERT: L 99 PHE cc_start: 0.6790 (m-80) cc_final: 0.6371 (m-80) REVERT: L 172 SER cc_start: 0.7191 (m) cc_final: 0.6806 (t) REVERT: A 65 ASN cc_start: 0.7723 (t0) cc_final: 0.7364 (p0) REVERT: A 78 ASN cc_start: -0.1795 (OUTLIER) cc_final: -0.4173 (t0) REVERT: A 200 TYR cc_start: 0.7007 (m-80) cc_final: 0.6467 (m-80) REVERT: A 201 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 306 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6295 (mtm-85) REVERT: A 353 SER cc_start: 0.8709 (m) cc_final: 0.8198 (p) REVERT: A 370 SER cc_start: 0.8373 (m) cc_final: 0.7964 (p) REVERT: A 416 PHE cc_start: 0.7108 (t80) cc_final: 0.6327 (t80) REVERT: A 454 ASP cc_start: 0.7582 (t70) cc_final: 0.7239 (t0) REVERT: A 537 VAL cc_start: 0.7942 (m) cc_final: 0.7638 (p) REVERT: A 545 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6605 (t80) outliers start: 42 outliers final: 26 residues processed: 186 average time/residue: 0.0798 time to fit residues: 20.2489 Evaluate side-chains 179 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR 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 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 360 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.0170 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 530 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.203748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179054 restraints weight = 13994.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.183508 restraints weight = 7608.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.186446 restraints weight = 4779.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.188514 restraints weight = 3340.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.189792 restraints weight = 2529.641| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5747 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7927 Z= 0.162 Angle : 0.638 9.847 10796 Z= 0.328 Chirality : 0.046 0.194 1202 Planarity : 0.005 0.049 1385 Dihedral : 7.043 69.802 1109 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.18 % Favored : 85.71 % Rotamer: Outliers : 5.55 % Allowed : 17.11 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.24), residues: 980 helix: -0.63 (0.95), residues: 35 sheet: -1.09 (0.34), residues: 254 loop : -3.26 (0.20), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 99 TYR 0.015 0.001 TYR H 152 PHE 0.024 0.002 PHE H 29 TRP 0.013 0.002 TRP A 340 HIS 0.003 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7916) covalent geometry : angle 0.63182 (10774) SS BOND : bond 0.00528 ( 11) SS BOND : angle 2.01740 ( 22) hydrogen bonds : bond 0.02902 ( 137) hydrogen bonds : angle 6.22667 ( 345) *********************** 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 196 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7098 (tt) REVERT: H 82 MET cc_start: 0.7433 (mtm) cc_final: 0.6904 (mpp) REVERT: H 106 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.4138 (p90) REVERT: L 11 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8132 (mp) REVERT: L 12 SER cc_start: 0.8736 (t) cc_final: 0.8351 (p) REVERT: L 99 PHE cc_start: 0.6706 (m-80) cc_final: 0.6357 (m-80) REVERT: L 172 SER cc_start: 0.7116 (m) cc_final: 0.6753 (t) REVERT: A 65 ASN cc_start: 0.7754 (t0) cc_final: 0.7430 (p0) REVERT: A 78 ASN cc_start: -0.1563 (OUTLIER) cc_final: -0.4024 (t0) REVERT: A 200 TYR cc_start: 0.6976 (m-80) cc_final: 0.6484 (m-80) REVERT: A 201 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 260 THR cc_start: 0.7803 (p) cc_final: 0.7483 (p) REVERT: A 306 ARG cc_start: 0.7225 (mtm-85) cc_final: 0.6374 (mtm-85) REVERT: A 353 SER cc_start: 0.8766 (m) cc_final: 0.8292 (p) REVERT: A 357 ASN cc_start: 0.7824 (t0) cc_final: 0.7623 (t0) REVERT: A 370 SER cc_start: 0.8497 (m) cc_final: 0.8091 (p) REVERT: A 416 PHE cc_start: 0.7034 (t80) cc_final: 0.6087 (t80) REVERT: A 454 ASP cc_start: 0.7629 (t70) cc_final: 0.7247 (t0) REVERT: A 465 LYS cc_start: 0.8458 (tppt) cc_final: 0.8208 (tppt) REVERT: A 537 VAL cc_start: 0.7962 (m) cc_final: 0.7643 (p) REVERT: A 545 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6652 (t80) outliers start: 48 outliers final: 25 residues processed: 186 average time/residue: 0.0815 time to fit residues: 20.7911 Evaluate side-chains 174 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 119 ILE 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 H residue 218 VAL Chi-restraints excluded: chain L residue 11 LEU 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 257 LEU Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 360 PHE 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 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 82 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN A 530 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.202595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.177898 restraints weight = 13842.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.182380 restraints weight = 7531.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.185358 restraints weight = 4739.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.187381 restraints weight = 3324.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188854 restraints weight = 2518.327| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7927 Z= 0.165 Angle : 0.664 10.571 10796 Z= 0.338 Chirality : 0.047 0.190 1202 Planarity : 0.005 0.050 1385 Dihedral : 7.136 71.832 1105 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.59 % Favored : 85.31 % Rotamer: Outliers : 5.32 % Allowed : 18.50 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.25), residues: 980 helix: -1.31 (0.87), residues: 42 sheet: -0.93 (0.35), residues: 251 loop : -3.14 (0.21), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.017 0.002 TYR H 94 PHE 0.024 0.002 PHE H 29 TRP 0.036 0.002 TRP H 36 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7916) covalent geometry : angle 0.65915 (10774) SS BOND : bond 0.00490 ( 11) SS BOND : angle 1.87216 ( 22) hydrogen bonds : bond 0.02927 ( 137) hydrogen bonds : angle 6.29129 ( 345) *********************** 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 192 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7182 (tt) REVERT: H 82 MET cc_start: 0.7574 (mtm) cc_final: 0.6922 (mtm) REVERT: H 106 TYR cc_start: 0.4614 (OUTLIER) cc_final: 0.4153 (p90) REVERT: L 3 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7948 (mm-40) REVERT: L 12 SER cc_start: 0.8699 (t) cc_final: 0.8384 (p) REVERT: L 99 PHE cc_start: 0.6753 (m-80) cc_final: 0.6375 (m-80) REVERT: L 172 SER cc_start: 0.7186 (m) cc_final: 0.6812 (t) REVERT: A 65 ASN cc_start: 0.7741 (t0) cc_final: 0.7395 (p0) REVERT: A 78 ASN cc_start: -0.1632 (OUTLIER) cc_final: -0.4063 (t0) REVERT: A 200 TYR cc_start: 0.7101 (m-80) cc_final: 0.6616 (m-80) REVERT: A 201 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7510 (tm-30) REVERT: A 306 ARG cc_start: 0.7242 (mtm-85) cc_final: 0.6507 (mtm-85) REVERT: A 341 GLU cc_start: 0.6216 (mm-30) cc_final: 0.5892 (mm-30) REVERT: A 353 SER cc_start: 0.8736 (m) cc_final: 0.8290 (p) REVERT: A 357 ASN cc_start: 0.7898 (t0) cc_final: 0.7623 (t0) REVERT: A 370 SER cc_start: 0.8531 (m) cc_final: 0.8021 (p) REVERT: A 416 PHE cc_start: 0.7068 (t80) cc_final: 0.6138 (t80) REVERT: A 454 ASP cc_start: 0.7596 (t70) cc_final: 0.7171 (t0) REVERT: A 537 VAL cc_start: 0.7913 (m) cc_final: 0.7584 (p) REVERT: A 545 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6659 (t80) outliers start: 46 outliers final: 32 residues processed: 181 average time/residue: 0.0847 time to fit residues: 20.5600 Evaluate side-chains 177 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 91 SER 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 253 PHE Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 401 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** A 530 ASN 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 = 0.202506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.177904 restraints weight = 13976.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.182361 restraints weight = 7635.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.185369 restraints weight = 4808.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.187447 restraints weight = 3343.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.188895 restraints weight = 2519.568| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7927 Z= 0.160 Angle : 0.673 11.279 10796 Z= 0.340 Chirality : 0.047 0.183 1202 Planarity : 0.005 0.049 1385 Dihedral : 7.177 74.474 1105 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.49 % Favored : 85.41 % Rotamer: Outliers : 5.09 % Allowed : 19.19 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.25), residues: 980 helix: -1.29 (0.88), residues: 42 sheet: -0.89 (0.35), residues: 253 loop : -3.08 (0.21), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.015 0.001 TYR H 152 PHE 0.020 0.002 PHE H 29 TRP 0.029 0.002 TRP H 36 HIS 0.004 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7916) covalent geometry : angle 0.66881 (10774) SS BOND : bond 0.00533 ( 11) SS BOND : angle 1.79381 ( 22) hydrogen bonds : bond 0.02906 ( 137) hydrogen bonds : angle 6.31567 ( 345) *********************** 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: 44 poor density : 142 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7176 (tt) REVERT: H 60 LEU cc_start: 0.7883 (tt) cc_final: 0.7563 (tt) REVERT: H 82 MET cc_start: 0.7556 (mtm) cc_final: 0.6979 (mtm) REVERT: H 106 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.4140 (p90) REVERT: H 170 VAL cc_start: 0.4561 (OUTLIER) cc_final: 0.4171 (m) REVERT: L 3 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7981 (mm-40) REVERT: L 12 SER cc_start: 0.8692 (t) cc_final: 0.8378 (p) REVERT: L 99 PHE cc_start: 0.6731 (m-80) cc_final: 0.6316 (m-80) REVERT: L 172 SER cc_start: 0.7176 (m) cc_final: 0.6796 (t) REVERT: A 65 ASN cc_start: 0.7785 (t0) cc_final: 0.7481 (p0) REVERT: A 78 ASN cc_start: -0.2285 (OUTLIER) cc_final: -0.4363 (t0) REVERT: A 200 TYR cc_start: 0.7122 (m-80) cc_final: 0.6679 (m-80) REVERT: A 201 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 306 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6534 (mtm-85) REVERT: A 341 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5886 (mm-30) REVERT: A 353 SER cc_start: 0.8756 (m) cc_final: 0.8317 (p) REVERT: A 357 ASN cc_start: 0.7909 (t0) cc_final: 0.7609 (t0) REVERT: A 370 SER cc_start: 0.8630 (m) cc_final: 0.8043 (p) REVERT: A 395 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6422 (mtm180) REVERT: A 416 PHE cc_start: 0.7045 (t80) cc_final: 0.6839 (t80) REVERT: A 454 ASP cc_start: 0.7457 (t70) cc_final: 0.7120 (t0) REVERT: A 537 VAL cc_start: 0.7903 (m) cc_final: 0.7579 (p) REVERT: A 545 PHE cc_start: 0.7135 (OUTLIER) cc_final: 0.6707 (t80) outliers start: 44 outliers final: 33 residues processed: 177 average time/residue: 0.0760 time to fit residues: 18.1277 Evaluate side-chains 179 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 104 ASN 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 22 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 138 ASN 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 219 ILE Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 401 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN A 155 ASN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.200595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.176361 restraints weight = 13850.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180792 restraints weight = 7585.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.183766 restraints weight = 4776.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.185810 restraints weight = 3327.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.187206 restraints weight = 2503.983| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7927 Z= 0.189 Angle : 0.707 11.796 10796 Z= 0.361 Chirality : 0.048 0.184 1202 Planarity : 0.005 0.050 1385 Dihedral : 7.176 75.861 1101 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 15.31 % Favored : 84.59 % Rotamer: Outliers : 5.09 % Allowed : 19.19 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.25), residues: 980 helix: -1.42 (0.79), residues: 48 sheet: -0.83 (0.35), residues: 253 loop : -3.09 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 143 TYR 0.018 0.002 TYR H 152 PHE 0.024 0.002 PHE H 29 TRP 0.028 0.002 TRP H 36 HIS 0.005 0.001 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 7916) covalent geometry : angle 0.70206 (10774) SS BOND : bond 0.00563 ( 11) SS BOND : angle 1.96451 ( 22) hydrogen bonds : bond 0.03069 ( 137) hydrogen bonds : angle 6.44579 ( 345) *********************** 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 194 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7223 (tt) REVERT: H 82 MET cc_start: 0.7512 (mtm) cc_final: 0.6911 (mtm) REVERT: H 106 TYR cc_start: 0.4586 (OUTLIER) cc_final: 0.4156 (p90) REVERT: H 107 TYR cc_start: 0.5101 (OUTLIER) cc_final: 0.4791 (m-80) REVERT: H 170 VAL cc_start: 0.4658 (OUTLIER) cc_final: 0.4287 (m) REVERT: L 3 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7822 (mm-40) REVERT: L 11 LEU cc_start: 0.8499 (mm) cc_final: 0.8224 (mp) REVERT: L 12 SER cc_start: 0.8710 (t) cc_final: 0.8383 (p) REVERT: L 99 PHE cc_start: 0.6763 (m-80) cc_final: 0.6378 (m-80) REVERT: L 172 SER cc_start: 0.7277 (m) cc_final: 0.6895 (t) REVERT: A 65 ASN cc_start: 0.7801 (t0) cc_final: 0.7541 (p0) REVERT: A 78 ASN cc_start: -0.1994 (OUTLIER) cc_final: -0.4150 (t0) REVERT: A 200 TYR cc_start: 0.7272 (m-80) cc_final: 0.6826 (m-80) REVERT: A 201 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7439 (tm-30) REVERT: A 306 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6993 (mtm-85) REVERT: A 341 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5903 (mm-30) REVERT: A 353 SER cc_start: 0.8769 (m) cc_final: 0.8358 (p) REVERT: A 357 ASN cc_start: 0.7918 (t0) cc_final: 0.7569 (t0) REVERT: A 395 ARG cc_start: 0.6996 (mtm110) cc_final: 0.6552 (mtm180) REVERT: A 416 PHE cc_start: 0.7081 (t80) cc_final: 0.6878 (t80) REVERT: A 454 ASP cc_start: 0.7454 (t70) cc_final: 0.7143 (t0) REVERT: A 537 VAL cc_start: 0.7849 (m) cc_final: 0.7519 (p) REVERT: A 545 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.7003 (t80) outliers start: 44 outliers final: 34 residues processed: 185 average time/residue: 0.0918 time to fit residues: 22.7933 Evaluate side-chains 187 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 TYR 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 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 22 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 138 ASN 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 219 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 520 ILE 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 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 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 0.0470 chunk 75 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 0.0030 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 overall best weight: 0.3288 ------------------------------------------------------------------------------- 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** A 523 GLN A 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.203291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.179225 restraints weight = 13908.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.183635 restraints weight = 7576.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.186615 restraints weight = 4768.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.188591 restraints weight = 3318.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.189978 restraints weight = 2510.376| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7927 Z= 0.124 Angle : 0.669 12.030 10796 Z= 0.337 Chirality : 0.047 0.230 1202 Planarity : 0.004 0.046 1385 Dihedral : 7.059 82.418 1101 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.08 % Favored : 85.82 % Rotamer: Outliers : 3.70 % Allowed : 20.92 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.26), residues: 980 helix: -1.28 (0.88), residues: 42 sheet: -0.61 (0.36), residues: 244 loop : -3.01 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 563 TYR 0.014 0.001 TYR A 481 PHE 0.019 0.001 PHE A 527 TRP 0.025 0.002 TRP H 36 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7916) covalent geometry : angle 0.66201 (10774) SS BOND : bond 0.00252 ( 11) SS BOND : angle 2.30338 ( 22) hydrogen bonds : bond 0.02563 ( 137) hydrogen bonds : angle 6.11310 ( 345) ********************** 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 172 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6967 (tt) REVERT: H 82 MET cc_start: 0.7574 (mtm) cc_final: 0.7005 (mtm) REVERT: H 106 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.4046 (p90) REVERT: H 170 VAL cc_start: 0.4601 (OUTLIER) cc_final: 0.4240 (m) REVERT: L 3 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7767 (mm-40) REVERT: L 11 LEU cc_start: 0.8518 (mm) cc_final: 0.8234 (mp) REVERT: L 12 SER cc_start: 0.8656 (t) cc_final: 0.8328 (p) REVERT: L 99 PHE cc_start: 0.6669 (m-80) cc_final: 0.6272 (m-80) REVERT: L 172 SER cc_start: 0.7112 (m) cc_final: 0.6754 (t) REVERT: A 65 ASN cc_start: 0.7822 (t0) cc_final: 0.7521 (p0) REVERT: A 78 ASN cc_start: -0.2125 (OUTLIER) cc_final: -0.4228 (t0) REVERT: A 200 TYR cc_start: 0.7124 (m-80) cc_final: 0.6757 (m-80) REVERT: A 306 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6933 (mtm-85) REVERT: A 341 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5816 (mm-30) REVERT: A 353 SER cc_start: 0.8724 (m) cc_final: 0.8312 (p) REVERT: A 357 ASN cc_start: 0.7862 (t0) cc_final: 0.7501 (t0) REVERT: A 370 SER cc_start: 0.8576 (m) cc_final: 0.8053 (p) REVERT: A 416 PHE cc_start: 0.6946 (t80) cc_final: 0.5972 (t80) REVERT: A 454 ASP cc_start: 0.7492 (t70) cc_final: 0.7147 (t0) REVERT: A 537 VAL cc_start: 0.7658 (m) cc_final: 0.7372 (p) REVERT: A 545 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6836 (t80) outliers start: 32 outliers final: 26 residues processed: 167 average time/residue: 0.0897 time to fit residues: 20.1281 Evaluate side-chains 171 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain H residue 136 LYS 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 26 SER 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 219 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 401 GLN Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 520 ILE 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 606 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 5 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.203553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.179534 restraints weight = 13893.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.183975 restraints weight = 7613.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.186959 restraints weight = 4784.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.188966 restraints weight = 3323.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.190363 restraints weight = 2512.417| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7927 Z= 0.123 Angle : 0.666 11.561 10796 Z= 0.335 Chirality : 0.047 0.219 1202 Planarity : 0.004 0.051 1385 Dihedral : 6.954 84.386 1100 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.78 % Favored : 86.12 % Rotamer: Outliers : 3.47 % Allowed : 21.50 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.26), residues: 980 helix: -1.19 (0.88), residues: 42 sheet: -0.57 (0.36), residues: 247 loop : -2.96 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 563 TYR 0.016 0.001 TYR A 481 PHE 0.019 0.001 PHE A 527 TRP 0.024 0.002 TRP H 36 HIS 0.002 0.000 HIS A 149 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7916) covalent geometry : angle 0.66042 (10774) SS BOND : bond 0.00289 ( 11) SS BOND : angle 2.06999 ( 22) hydrogen bonds : bond 0.02435 ( 137) hydrogen bonds : angle 5.98628 ( 345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1501.22 seconds wall clock time: 26 minutes 34.85 seconds (1594.85 seconds total)