Starting phenix.real_space_refine on Mon Apr 28 15:50:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kek_37161/04_2025/8kek_37161.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kek_37161/04_2025/8kek_37161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kek_37161/04_2025/8kek_37161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kek_37161/04_2025/8kek_37161.map" model { file = "/net/cci-nas-00/data/ceres_data/8kek_37161/04_2025/8kek_37161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kek_37161/04_2025/8kek_37161.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4921 2.51 5 N 1285 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7721 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1630 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "A" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4460 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 32, 'TRANS': 532} Chain breaks: 4 Time building chain proxies: 5.17, per 1000 atoms: 0.67 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 19 sheets defined 5.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 190 removed outlier: 3.580A pdb=" N HIS L 190 " --> pdb=" O ASP L 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.667A pdb=" N GLY A 270 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 removed outlier: 3.545A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.538A pdb=" N VAL A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 329' Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.809A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 605 through 612 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.740A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER H 77 " --> pdb=" O GLU H 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 50 through 51 removed outlier: 3.547A pdb=" N ILE H 34 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA H 91 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AA4, first strand: chain 'H' and resid 202 through 203 removed outlier: 3.944A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.729A pdb=" N GLU L 106 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 21 through 22 removed outlier: 4.314A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.104A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.920A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.783A pdb=" N TRP L 149 " --> pdb=" O GLN L 156 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 198 " --> pdb=" O LYS L 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.705A pdb=" N TYR A 53 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.912A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 87 through 91 removed outlier: 4.010A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 187 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 197 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.276A pdb=" N ILE A 117 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 124 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 119 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 163 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.643A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 300 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 583 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 595 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 312 through 313 removed outlier: 3.623A pdb=" N GLY A 536 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 341 through 345 removed outlier: 4.018A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 386 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 500 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.518A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.629A pdb=" N TYR A 440 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 479 " --> pdb=" O TYR A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 551 through 553 137 hydrogen bonds defined for protein. 345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 2.10 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.560 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7927 Z= 0.107 Angle : 0.490 8.333 10796 Z= 0.265 Chirality : 0.042 0.140 1202 Planarity : 0.003 0.038 1385 Dihedral : 9.406 78.054 2814 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.92 % Favored : 88.98 % Rotamer: Outliers : 6.01 % Allowed : 6.94 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.21), residues: 980 helix: -2.59 (0.70), residues: 35 sheet: -2.68 (0.30), residues: 248 loop : -4.02 (0.18), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 423 HIS 0.004 0.000 HIS H 35 PHE 0.007 0.001 PHE A 360 TYR 0.004 0.001 TYR H 108 ARG 0.001 0.000 ARG A 495 Details of bonding type rmsd hydrogen bonds : bond 0.29211 ( 137) hydrogen bonds : angle 12.08951 ( 345) SS BOND : bond 0.00122 ( 11) SS BOND : angle 0.48191 ( 22) covalent geometry : bond 0.00209 ( 7916) covalent geometry : angle 0.48976 (10774) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.791 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: 0.2231 time to fit residues: 67.9799 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 : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN H 81 GLN H 104 ASN H 171 HIS H 178 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 101 GLN L 156 GLN A 33 HIS A 70 HIS ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 GLN A 427 ASN A 530 ASN A 550 GLN A 632 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.212406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.187310 restraints weight = 14202.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.191731 restraints weight = 7748.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.194574 restraints weight = 4928.931| |-----------------------------------------------------------------------------| r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7927 Z= 0.142 Angle : 0.622 9.665 10796 Z= 0.317 Chirality : 0.046 0.173 1202 Planarity : 0.005 0.042 1385 Dihedral : 6.876 59.170 1120 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.06 % Favored : 86.84 % Rotamer: Outliers : 5.20 % Allowed : 13.06 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.23), residues: 980 helix: -2.06 (0.82), residues: 35 sheet: -1.90 (0.31), residues: 255 loop : -3.70 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 101 HIS 0.007 0.001 HIS A 70 PHE 0.035 0.002 PHE H 29 TYR 0.013 0.001 TYR H 59 ARG 0.006 0.001 ARG A 306 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 137) hydrogen bonds : angle 7.86631 ( 345) SS BOND : bond 0.00309 ( 11) SS BOND : angle 2.02626 ( 22) covalent geometry : bond 0.00340 ( 7916) covalent geometry : angle 0.61574 (10774) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8070 (t) cc_final: 0.7749 (p) REVERT: H 18 LEU cc_start: 0.7639 (tt) cc_final: 0.7048 (tp) REVERT: H 82 MET cc_start: 0.7043 (mtm) cc_final: 0.6743 (mpp) REVERT: H 104 ASN cc_start: 0.6535 (OUTLIER) cc_final: 0.6312 (p0) REVERT: H 106 TYR cc_start: 0.4507 (OUTLIER) cc_final: 0.4126 (p90) REVERT: L 12 SER cc_start: 0.8672 (t) cc_final: 0.8394 (p) REVERT: L 75 ILE cc_start: 0.8272 (mt) cc_final: 0.8057 (mt) REVERT: L 92 TYR cc_start: 0.7925 (t80) cc_final: 0.7504 (t80) REVERT: L 99 PHE cc_start: 0.6715 (m-80) cc_final: 0.6424 (m-80) REVERT: L 143 ARG cc_start: 0.7181 (tmm160) cc_final: 0.6913 (tmt170) REVERT: L 172 SER cc_start: 0.7175 (m) cc_final: 0.6823 (t) REVERT: A 53 TYR cc_start: 0.7132 (t80) cc_final: 0.6612 (t80) REVERT: A 65 ASN cc_start: 0.7836 (t0) cc_final: 0.7586 (p0) REVERT: A 78 ASN cc_start: -0.2085 (OUTLIER) cc_final: -0.4464 (t0) REVERT: A 99 ARG cc_start: 0.5827 (ptm160) cc_final: 0.5613 (ptm160) REVERT: A 260 THR cc_start: 0.7897 (p) cc_final: 0.7536 (p) REVERT: A 353 SER cc_start: 0.8622 (m) cc_final: 0.8135 (t) REVERT: A 370 SER cc_start: 0.8418 (m) cc_final: 0.8057 (p) REVERT: A 389 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (t) REVERT: A 412 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7521 (mp) REVERT: A 416 PHE cc_start: 0.7192 (t80) cc_final: 0.6704 (t80) REVERT: A 424 ASN cc_start: 0.8117 (t0) cc_final: 0.7891 (t0) REVERT: A 454 ASP cc_start: 0.7667 (t70) cc_final: 0.7351 (t0) REVERT: A 545 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6296 (t80) outliers start: 45 outliers final: 26 residues processed: 204 average time/residue: 0.2145 time to fit residues: 57.2882 Evaluate side-chains 193 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN A 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.209834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.184730 restraints weight = 14243.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.189226 restraints weight = 7699.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.192168 restraints weight = 4855.567| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 7927 Z= 0.129 Angle : 0.607 8.628 10796 Z= 0.308 Chirality : 0.045 0.186 1202 Planarity : 0.004 0.042 1385 Dihedral : 6.752 60.866 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.65 % Favored : 87.24 % Rotamer: Outliers : 5.43 % Allowed : 14.34 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.24), residues: 980 helix: -2.35 (0.74), residues: 41 sheet: -1.43 (0.33), residues: 256 loop : -3.54 (0.20), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 112 HIS 0.002 0.000 HIS A 149 PHE 0.035 0.001 PHE H 29 TYR 0.011 0.001 TYR H 94 ARG 0.003 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 137) hydrogen bonds : angle 6.92709 ( 345) SS BOND : bond 0.00492 ( 11) SS BOND : angle 1.93091 ( 22) covalent geometry : bond 0.00311 ( 7916) covalent geometry : angle 0.60109 (10774) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8021 (t) cc_final: 0.7782 (p) REVERT: H 18 LEU cc_start: 0.7633 (tt) cc_final: 0.7042 (tp) REVERT: H 82 MET cc_start: 0.7237 (mtm) cc_final: 0.7000 (mpp) REVERT: H 106 TYR cc_start: 0.4489 (OUTLIER) cc_final: 0.4161 (p90) REVERT: L 12 SER cc_start: 0.8781 (t) cc_final: 0.8444 (p) REVERT: L 76 SER cc_start: 0.7528 (m) cc_final: 0.7171 (p) REVERT: L 92 TYR cc_start: 0.7924 (t80) cc_final: 0.7478 (t80) REVERT: L 99 PHE cc_start: 0.6724 (m-80) cc_final: 0.6401 (m-80) REVERT: L 143 ARG cc_start: 0.7360 (tmm160) cc_final: 0.7092 (tpt170) REVERT: L 172 SER cc_start: 0.7078 (m) cc_final: 0.6757 (t) REVERT: A 53 TYR cc_start: 0.7302 (t80) cc_final: 0.6807 (t80) REVERT: A 65 ASN cc_start: 0.7807 (t0) cc_final: 0.7504 (p0) REVERT: A 78 ASN cc_start: -0.2064 (OUTLIER) cc_final: -0.4432 (t0) REVERT: A 99 ARG cc_start: 0.5795 (ptm160) cc_final: 0.5580 (ptm160) REVERT: A 260 THR cc_start: 0.7836 (p) cc_final: 0.7492 (p) REVERT: A 306 ARG cc_start: 0.7191 (mtm-85) cc_final: 0.6374 (mtm-85) REVERT: A 353 SER cc_start: 0.8651 (m) cc_final: 0.8146 (p) REVERT: A 370 SER cc_start: 0.8399 (m) cc_final: 0.8045 (p) REVERT: A 389 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.6176 (t) REVERT: A 416 PHE cc_start: 0.7281 (t80) cc_final: 0.6956 (t80) REVERT: A 424 ASN cc_start: 0.8123 (t0) cc_final: 0.7877 (t0) REVERT: A 454 ASP cc_start: 0.7679 (t70) cc_final: 0.7335 (t0) REVERT: A 537 VAL cc_start: 0.7838 (m) cc_final: 0.7491 (p) REVERT: A 545 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6358 (t80) outliers start: 47 outliers final: 28 residues processed: 197 average time/residue: 0.2076 time to fit residues: 54.9778 Evaluate side-chains 188 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 ASN A 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.206673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.181451 restraints weight = 13885.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.185859 restraints weight = 7534.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.188872 restraints weight = 4775.461| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7927 Z= 0.154 Angle : 0.619 8.905 10796 Z= 0.318 Chirality : 0.046 0.159 1202 Planarity : 0.005 0.048 1385 Dihedral : 7.088 67.956 1114 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.98 % Favored : 85.92 % Rotamer: Outliers : 5.78 % Allowed : 15.14 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.24), residues: 980 helix: -1.29 (0.86), residues: 35 sheet: -1.20 (0.33), residues: 246 loop : -3.44 (0.20), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.003 0.001 HIS A 149 PHE 0.023 0.002 PHE H 29 TYR 0.015 0.001 TYR H 94 ARG 0.003 0.000 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 137) hydrogen bonds : angle 6.50790 ( 345) SS BOND : bond 0.00318 ( 11) SS BOND : angle 1.69178 ( 22) covalent geometry : bond 0.00357 ( 7916) covalent geometry : angle 0.61516 (10774) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 159 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.7326 (mtm) cc_final: 0.7048 (mpp) REVERT: H 106 TYR cc_start: 0.4477 (OUTLIER) cc_final: 0.4107 (p90) REVERT: L 12 SER cc_start: 0.8712 (t) cc_final: 0.8351 (p) REVERT: L 76 SER cc_start: 0.7463 (m) cc_final: 0.7247 (p) REVERT: L 99 PHE cc_start: 0.6764 (m-80) cc_final: 0.6408 (m-80) REVERT: L 143 ARG cc_start: 0.7474 (tmm160) cc_final: 0.7086 (tpt170) REVERT: L 166 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7415 (tm-30) REVERT: L 172 SER cc_start: 0.7139 (m) cc_final: 0.6787 (t) REVERT: A 53 TYR cc_start: 0.7307 (t80) cc_final: 0.6734 (t80) REVERT: A 65 ASN cc_start: 0.7682 (t0) cc_final: 0.7400 (p0) REVERT: A 78 ASN cc_start: -0.1755 (OUTLIER) cc_final: -0.4159 (t0) REVERT: A 200 TYR cc_start: 0.6982 (m-80) cc_final: 0.6508 (m-80) REVERT: A 201 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7277 (tm-30) REVERT: A 260 THR cc_start: 0.7798 (p) cc_final: 0.7439 (p) REVERT: A 306 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6323 (mtm-85) REVERT: A 353 SER cc_start: 0.8777 (m) cc_final: 0.8290 (p) REVERT: A 357 ASN cc_start: 0.7911 (t0) cc_final: 0.7510 (t0) REVERT: A 370 SER cc_start: 0.8372 (m) cc_final: 0.8018 (p) REVERT: A 412 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7624 (mp) REVERT: A 416 PHE cc_start: 0.7265 (t80) cc_final: 0.6983 (t80) REVERT: A 454 ASP cc_start: 0.7644 (t70) cc_final: 0.7269 (t0) REVERT: A 537 VAL cc_start: 0.7939 (m) cc_final: 0.7606 (p) REVERT: A 545 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.6575 (t80) outliers start: 50 outliers final: 26 residues processed: 198 average time/residue: 0.2196 time to fit residues: 57.5265 Evaluate side-chains 182 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 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 412 LEU Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 0.0000 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.0040 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 overall best weight: 0.2154 ------------------------------------------------------------------------------- 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 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.208789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.183797 restraints weight = 14074.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.188230 restraints weight = 7583.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.191258 restraints weight = 4756.607| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5716 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7927 Z= 0.105 Angle : 0.584 9.077 10796 Z= 0.293 Chirality : 0.045 0.181 1202 Planarity : 0.004 0.044 1385 Dihedral : 6.803 73.741 1106 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.65 % Favored : 87.24 % Rotamer: Outliers : 4.51 % Allowed : 17.11 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.24), residues: 980 helix: -1.07 (0.89), residues: 36 sheet: -1.21 (0.33), residues: 267 loop : -3.31 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 97 HIS 0.002 0.000 HIS L 37 PHE 0.021 0.001 PHE H 153 TYR 0.011 0.001 TYR A 481 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02507 ( 137) hydrogen bonds : angle 5.98004 ( 345) SS BOND : bond 0.00192 ( 11) SS BOND : angle 1.55642 ( 22) covalent geometry : bond 0.00251 ( 7916) covalent geometry : angle 0.58060 (10774) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6787 (tt) REVERT: H 18 LEU cc_start: 0.7613 (tt) cc_final: 0.6910 (tp) REVERT: H 82 MET cc_start: 0.7391 (mtm) cc_final: 0.7142 (mpp) REVERT: H 106 TYR cc_start: 0.4516 (OUTLIER) cc_final: 0.4119 (p90) REVERT: L 12 SER cc_start: 0.8694 (t) cc_final: 0.8309 (p) REVERT: L 76 SER cc_start: 0.7539 (m) cc_final: 0.7121 (p) REVERT: L 92 TYR cc_start: 0.7725 (t80) cc_final: 0.7397 (t80) REVERT: L 99 PHE cc_start: 0.6679 (m-80) cc_final: 0.6323 (m-80) REVERT: L 166 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7379 (tm-30) REVERT: L 172 SER cc_start: 0.7046 (m) cc_final: 0.6736 (t) REVERT: L 174 TYR cc_start: 0.7088 (m-80) cc_final: 0.6336 (m-10) REVERT: A 65 ASN cc_start: 0.7758 (t0) cc_final: 0.7401 (p0) REVERT: A 78 ASN cc_start: -0.1746 (OUTLIER) cc_final: -0.4075 (t0) REVERT: A 200 TYR cc_start: 0.6882 (m-80) cc_final: 0.6434 (m-80) REVERT: A 201 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7330 (tm-30) REVERT: A 260 THR cc_start: 0.7754 (p) cc_final: 0.7464 (p) REVERT: A 306 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6288 (mtm-85) REVERT: A 353 SER cc_start: 0.8707 (m) cc_final: 0.8227 (p) REVERT: A 357 ASN cc_start: 0.7842 (t0) cc_final: 0.7464 (t0) REVERT: A 370 SER cc_start: 0.8350 (m) cc_final: 0.7987 (p) REVERT: A 454 ASP cc_start: 0.7612 (t70) cc_final: 0.7235 (t0) REVERT: A 537 VAL cc_start: 0.7752 (m) cc_final: 0.7444 (p) REVERT: A 545 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6439 (t80) outliers start: 39 outliers final: 22 residues processed: 186 average time/residue: 0.2148 time to fit residues: 53.0979 Evaluate side-chains 177 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 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 A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 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 = 0.4533 r_free = 0.4533 target = 0.202420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.178108 restraints weight = 13646.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.182477 restraints weight = 7388.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.185471 restraints weight = 4663.625| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7927 Z= 0.178 Angle : 0.661 10.375 10796 Z= 0.338 Chirality : 0.047 0.175 1202 Planarity : 0.005 0.051 1385 Dihedral : 6.990 71.262 1103 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.69 % Favored : 85.20 % Rotamer: Outliers : 5.20 % Allowed : 16.76 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.25), residues: 980 helix: -0.89 (0.94), residues: 36 sheet: -1.06 (0.33), residues: 262 loop : -3.22 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.003 0.001 HIS L 199 PHE 0.027 0.002 PHE H 153 TYR 0.019 0.002 TYR H 152 ARG 0.003 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 137) hydrogen bonds : angle 6.28864 ( 345) SS BOND : bond 0.00437 ( 11) SS BOND : angle 1.07954 ( 22) covalent geometry : bond 0.00405 ( 7916) covalent geometry : angle 0.66016 (10774) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7252 (tt) REVERT: H 82 MET cc_start: 0.7508 (mtm) cc_final: 0.6868 (mpp) REVERT: H 106 TYR cc_start: 0.4584 (OUTLIER) cc_final: 0.4118 (p90) REVERT: L 12 SER cc_start: 0.8670 (t) cc_final: 0.8342 (p) REVERT: L 31 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6819 (ptpt) REVERT: L 99 PHE cc_start: 0.6793 (m-80) cc_final: 0.6370 (m-80) REVERT: L 172 SER cc_start: 0.7251 (m) cc_final: 0.6854 (t) REVERT: A 65 ASN cc_start: 0.7670 (t0) cc_final: 0.7385 (p0) REVERT: A 78 ASN cc_start: -0.1567 (OUTLIER) cc_final: -0.4049 (t0) REVERT: A 200 TYR cc_start: 0.7107 (m-80) cc_final: 0.6573 (m-80) REVERT: A 201 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 306 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.6490 (mtm-85) REVERT: A 353 SER cc_start: 0.8771 (m) cc_final: 0.8315 (p) REVERT: A 357 ASN cc_start: 0.7939 (t0) cc_final: 0.7577 (t0) REVERT: A 370 SER cc_start: 0.8557 (m) cc_final: 0.7984 (p) REVERT: A 395 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6815 (mtm180) REVERT: A 416 PHE cc_start: 0.7023 (t80) cc_final: 0.6511 (t80) REVERT: A 424 ASN cc_start: 0.8207 (t0) cc_final: 0.7851 (t0) REVERT: A 454 ASP cc_start: 0.7581 (t70) cc_final: 0.7200 (t0) REVERT: A 465 LYS cc_start: 0.8460 (tppt) cc_final: 0.8140 (tppt) REVERT: A 537 VAL cc_start: 0.7878 (m) cc_final: 0.7549 (p) REVERT: A 545 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6690 (t80) outliers start: 45 outliers final: 29 residues processed: 189 average time/residue: 0.2298 time to fit residues: 57.9658 Evaluate side-chains 187 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 138 ASN Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.0010 chunk 95 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.0670 overall best weight: 0.3724 ------------------------------------------------------------------------------- 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** L 125 GLN A 33 HIS A 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.204799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180409 restraints weight = 13757.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.184862 restraints weight = 7437.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.187895 restraints weight = 4619.697| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7927 Z= 0.118 Angle : 0.630 10.588 10796 Z= 0.313 Chirality : 0.046 0.176 1202 Planarity : 0.004 0.045 1385 Dihedral : 6.941 77.614 1103 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.37 % Favored : 86.53 % Rotamer: Outliers : 4.05 % Allowed : 19.19 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.25), residues: 980 helix: -1.44 (0.85), residues: 42 sheet: -0.83 (0.35), residues: 250 loop : -3.06 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 36 HIS 0.002 0.000 HIS A 149 PHE 0.021 0.001 PHE H 29 TYR 0.012 0.001 TYR L 193 ARG 0.003 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02524 ( 137) hydrogen bonds : angle 6.04526 ( 345) SS BOND : bond 0.00554 ( 11) SS BOND : angle 1.00967 ( 22) covalent geometry : bond 0.00276 ( 7916) covalent geometry : angle 0.62869 (10774) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6889 (tt) REVERT: H 82 MET cc_start: 0.7505 (mtm) cc_final: 0.7031 (mtm) REVERT: H 106 TYR cc_start: 0.4493 (OUTLIER) cc_final: 0.4071 (p90) REVERT: L 12 SER cc_start: 0.8668 (t) cc_final: 0.8330 (p) REVERT: L 31 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6929 (ptpt) REVERT: L 99 PHE cc_start: 0.6717 (m-80) cc_final: 0.6276 (m-80) REVERT: L 172 SER cc_start: 0.7076 (m) cc_final: 0.6723 (t) REVERT: A 65 ASN cc_start: 0.7779 (t0) cc_final: 0.7472 (p0) REVERT: A 78 ASN cc_start: -0.1997 (OUTLIER) cc_final: -0.4166 (t0) REVERT: A 200 TYR cc_start: 0.7049 (m-80) cc_final: 0.6608 (m-80) REVERT: A 201 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 306 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6427 (mtm-85) REVERT: A 353 SER cc_start: 0.8723 (m) cc_final: 0.8293 (p) REVERT: A 357 ASN cc_start: 0.7919 (t0) cc_final: 0.7567 (t0) REVERT: A 370 SER cc_start: 0.8483 (m) cc_final: 0.8011 (p) REVERT: A 416 PHE cc_start: 0.6989 (t80) cc_final: 0.6428 (t80) REVERT: A 424 ASN cc_start: 0.8307 (t0) cc_final: 0.8027 (t0) REVERT: A 454 ASP cc_start: 0.7450 (t70) cc_final: 0.7106 (t0) REVERT: A 465 LYS cc_start: 0.8357 (tppt) cc_final: 0.8047 (tppt) REVERT: A 537 VAL cc_start: 0.7822 (m) cc_final: 0.7512 (p) outliers start: 35 outliers final: 23 residues processed: 174 average time/residue: 0.2026 time to fit residues: 47.2629 Evaluate side-chains 172 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 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 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 146 LYS Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 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 468 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.202060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.177846 restraints weight = 13773.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.182283 restraints weight = 7459.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185210 restraints weight = 4679.658| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7927 Z= 0.161 Angle : 0.669 10.605 10796 Z= 0.337 Chirality : 0.047 0.188 1202 Planarity : 0.005 0.049 1385 Dihedral : 6.912 76.433 1101 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.49 % Favored : 85.41 % Rotamer: Outliers : 4.28 % Allowed : 18.61 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.25), residues: 980 helix: -1.85 (0.78), residues: 48 sheet: -0.79 (0.35), residues: 252 loop : -3.00 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 36 HIS 0.004 0.001 HIS A 149 PHE 0.021 0.002 PHE H 29 TYR 0.016 0.002 TYR H 94 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02742 ( 137) hydrogen bonds : angle 6.22772 ( 345) SS BOND : bond 0.00377 ( 11) SS BOND : angle 1.37979 ( 22) covalent geometry : bond 0.00371 ( 7916) covalent geometry : angle 0.66639 (10774) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7197 (tt) REVERT: H 60 LEU cc_start: 0.7934 (tt) cc_final: 0.7623 (tt) REVERT: H 82 MET cc_start: 0.7517 (mtm) cc_final: 0.6968 (mtm) REVERT: H 106 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.4085 (p90) REVERT: H 107 TYR cc_start: 0.4990 (OUTLIER) cc_final: 0.4736 (m-80) REVERT: H 170 VAL cc_start: 0.4665 (OUTLIER) cc_final: 0.4278 (m) REVERT: L 3 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7954 (mm-40) REVERT: L 12 SER cc_start: 0.8659 (t) cc_final: 0.8331 (p) REVERT: L 31 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6868 (ptpt) REVERT: L 99 PHE cc_start: 0.6766 (m-80) cc_final: 0.6363 (m-80) REVERT: L 172 SER cc_start: 0.7122 (m) cc_final: 0.6769 (t) REVERT: A 65 ASN cc_start: 0.7787 (t0) cc_final: 0.7491 (p0) REVERT: A 78 ASN cc_start: -0.2076 (OUTLIER) cc_final: -0.4245 (t0) REVERT: A 200 TYR cc_start: 0.7167 (m-80) cc_final: 0.6673 (m-80) REVERT: A 201 GLN cc_start: 0.7753 (tm-30) cc_final: 0.7521 (tm-30) REVERT: A 306 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6954 (mtm-85) REVERT: A 353 SER cc_start: 0.8765 (m) cc_final: 0.8350 (p) REVERT: A 357 ASN cc_start: 0.7945 (t0) cc_final: 0.7605 (t0) REVERT: A 416 PHE cc_start: 0.6964 (t80) cc_final: 0.6414 (t80) REVERT: A 417 MET cc_start: 0.7425 (tpp) cc_final: 0.7212 (tpp) REVERT: A 424 ASN cc_start: 0.8327 (t0) cc_final: 0.8012 (t0) REVERT: A 454 ASP cc_start: 0.7468 (t70) cc_final: 0.7158 (t0) REVERT: A 520 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 537 VAL cc_start: 0.7933 (m) cc_final: 0.7591 (p) outliers start: 37 outliers final: 26 residues processed: 180 average time/residue: 0.2268 time to fit residues: 54.4626 Evaluate side-chains 178 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 635 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.202922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.178625 restraints weight = 13911.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.183114 restraints weight = 7519.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.186109 restraints weight = 4692.786| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7927 Z= 0.136 Angle : 0.673 11.742 10796 Z= 0.335 Chirality : 0.046 0.180 1202 Planarity : 0.005 0.046 1385 Dihedral : 6.712 80.664 1097 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.59 % Favored : 85.31 % Rotamer: Outliers : 4.39 % Allowed : 19.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.25), residues: 980 helix: -1.25 (0.87), residues: 42 sheet: -0.59 (0.36), residues: 243 loop : -3.00 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.004 0.001 HIS A 149 PHE 0.020 0.001 PHE H 29 TYR 0.016 0.001 TYR A 481 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02578 ( 137) hydrogen bonds : angle 6.20618 ( 345) SS BOND : bond 0.00324 ( 11) SS BOND : angle 1.15806 ( 22) covalent geometry : bond 0.00317 ( 7916) covalent geometry : angle 0.67215 (10774) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.7071 (tt) REVERT: H 60 LEU cc_start: 0.7873 (tt) cc_final: 0.7559 (tt) REVERT: H 82 MET cc_start: 0.7519 (mtm) cc_final: 0.6970 (mtm) REVERT: H 106 TYR cc_start: 0.4414 (OUTLIER) cc_final: 0.4084 (p90) REVERT: H 170 VAL cc_start: 0.4684 (OUTLIER) cc_final: 0.4313 (m) REVERT: L 3 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7967 (mm-40) REVERT: L 12 SER cc_start: 0.8643 (t) cc_final: 0.8297 (p) REVERT: L 99 PHE cc_start: 0.6725 (m-80) cc_final: 0.6273 (m-80) REVERT: L 172 SER cc_start: 0.7072 (m) cc_final: 0.6737 (t) REVERT: A 65 ASN cc_start: 0.7786 (t0) cc_final: 0.7529 (p0) REVERT: A 78 ASN cc_start: -0.1810 (OUTLIER) cc_final: -0.4028 (t0) REVERT: A 200 TYR cc_start: 0.7134 (m-80) cc_final: 0.6678 (m-80) REVERT: A 201 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 306 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6930 (mtm-85) REVERT: A 353 SER cc_start: 0.8756 (m) cc_final: 0.8344 (p) REVERT: A 357 ASN cc_start: 0.7889 (t0) cc_final: 0.7558 (t0) REVERT: A 416 PHE cc_start: 0.6929 (t80) cc_final: 0.6330 (t80) REVERT: A 417 MET cc_start: 0.7362 (tpp) cc_final: 0.7160 (tpp) REVERT: A 424 ASN cc_start: 0.8332 (t0) cc_final: 0.8009 (t0) REVERT: A 454 ASP cc_start: 0.7485 (t70) cc_final: 0.7164 (t0) REVERT: A 520 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7788 (mt) REVERT: A 537 VAL cc_start: 0.7758 (m) cc_final: 0.7444 (p) outliers start: 38 outliers final: 29 residues processed: 176 average time/residue: 0.2364 time to fit residues: 57.1346 Evaluate side-chains 180 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 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 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 260 THR 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 65 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.0170 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.202074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.178165 restraints weight = 13859.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.182546 restraints weight = 7542.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.185538 restraints weight = 4752.160| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7927 Z= 0.147 Angle : 0.684 11.613 10796 Z= 0.342 Chirality : 0.047 0.192 1202 Planarity : 0.005 0.048 1385 Dihedral : 6.458 81.706 1095 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.59 % Favored : 85.31 % Rotamer: Outliers : 4.05 % Allowed : 20.12 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.26), residues: 980 helix: -1.15 (0.86), residues: 42 sheet: -0.56 (0.36), residues: 244 loop : -2.93 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 36 HIS 0.003 0.001 HIS A 149 PHE 0.021 0.002 PHE H 29 TYR 0.019 0.002 TYR A 481 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02585 ( 137) hydrogen bonds : angle 6.24876 ( 345) SS BOND : bond 0.00373 ( 11) SS BOND : angle 1.37688 ( 22) covalent geometry : bond 0.00339 ( 7916) covalent geometry : angle 0.68221 (10774) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7102 (tt) REVERT: H 60 LEU cc_start: 0.7914 (tt) cc_final: 0.7618 (tt) REVERT: H 82 MET cc_start: 0.7467 (mtm) cc_final: 0.6881 (mtm) REVERT: H 106 TYR cc_start: 0.4417 (OUTLIER) cc_final: 0.4108 (p90) REVERT: H 170 VAL cc_start: 0.4652 (OUTLIER) cc_final: 0.4297 (m) REVERT: L 3 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7965 (mm-40) REVERT: L 12 SER cc_start: 0.8689 (t) cc_final: 0.8301 (p) REVERT: L 99 PHE cc_start: 0.6728 (m-80) cc_final: 0.6298 (m-80) REVERT: L 172 SER cc_start: 0.7085 (m) cc_final: 0.6746 (t) REVERT: A 65 ASN cc_start: 0.7792 (t0) cc_final: 0.7535 (p0) REVERT: A 78 ASN cc_start: -0.1910 (OUTLIER) cc_final: -0.4090 (t0) REVERT: A 200 TYR cc_start: 0.7199 (m-80) cc_final: 0.6786 (m-80) REVERT: A 306 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6355 (mtm-85) REVERT: A 353 SER cc_start: 0.8756 (m) cc_final: 0.8360 (p) REVERT: A 357 ASN cc_start: 0.7901 (t0) cc_final: 0.7570 (t0) REVERT: A 416 PHE cc_start: 0.6905 (t80) cc_final: 0.6288 (t80) REVERT: A 424 ASN cc_start: 0.8316 (t0) cc_final: 0.8051 (t0) REVERT: A 454 ASP cc_start: 0.7494 (t70) cc_final: 0.7198 (t0) REVERT: A 537 VAL cc_start: 0.7763 (m) cc_final: 0.7459 (p) outliers start: 35 outliers final: 28 residues processed: 173 average time/residue: 0.2041 time to fit residues: 47.7919 Evaluate side-chains 176 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 85 LEU Chi-restraints excluded: chain H residue 106 TYR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 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 21 optimal weight: 0.1980 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.202519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178374 restraints weight = 13975.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.182860 restraints weight = 7570.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.185818 restraints weight = 4756.995| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7927 Z= 0.134 Angle : 0.682 12.430 10796 Z= 0.336 Chirality : 0.046 0.186 1202 Planarity : 0.005 0.046 1385 Dihedral : 6.382 85.925 1095 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.18 % Favored : 85.71 % Rotamer: Outliers : 3.58 % Allowed : 20.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.26), residues: 980 helix: -0.98 (0.86), residues: 42 sheet: -0.49 (0.36), residues: 243 loop : -2.88 (0.21), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 36 HIS 0.002 0.001 HIS A 149 PHE 0.016 0.001 PHE H 27 TYR 0.019 0.001 TYR A 481 ARG 0.004 0.000 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.02469 ( 137) hydrogen bonds : angle 6.15343 ( 345) SS BOND : bond 0.00310 ( 11) SS BOND : angle 1.12925 ( 22) covalent geometry : bond 0.00311 ( 7916) covalent geometry : angle 0.68047 (10774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3139.46 seconds wall clock time: 55 minutes 43.89 seconds (3343.89 seconds total)