Starting phenix.real_space_refine on Thu May 1 02:06:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9y_39085/05_2025/8y9y_39085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9y_39085/05_2025/8y9y_39085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9y_39085/05_2025/8y9y_39085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9y_39085/05_2025/8y9y_39085.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9y_39085/05_2025/8y9y_39085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9y_39085/05_2025/8y9y_39085.cif" } resolution = 3.29 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= 0.000 sd= 0.005 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: 8 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 48 5.16 5 Be 1 3.05 5 C 6534 2.51 5 N 1741 2.21 5 O 1877 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10207 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6107 Classifications: {'peptide': 765} Link IDs: {'PTRANS': 15, 'TRANS': 749} Chain: "Y" Number of atoms: 3188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3188 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 20, 'TRANS': 388} Chain breaks: 2 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.07, per 1000 atoms: 0.59 Number of scatterers: 10207 At special positions: 0 Unit cell: (123.669, 98.301, 112.042, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 2 15.00 Mg 1 11.99 F 3 9.00 O 1877 8.00 N 1741 7.00 C 6534 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Y 60 " - pdb=" SG CYS B 26 " distance=2.04 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 9 sheets defined 66.6% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 15 through 34 removed outlier: 3.501A pdb=" N TYR A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.539A pdb=" N GLY A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 78 removed outlier: 4.050A pdb=" N VAL A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 130 through 148 removed outlier: 3.731A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.621A pdb=" N ASN A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.531A pdb=" N GLN A 195 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.587A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.634A pdb=" N ASP A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 306' Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 377 through 384 Processing helix chain 'A' and resid 410 through 427 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.831A pdb=" N SER A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 451 " --> pdb=" O LYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.631A pdb=" N GLY A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG A 489 " --> pdb=" O MET A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 489' Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.985A pdb=" N ASP A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 554 through 562 removed outlier: 4.291A pdb=" N GLY A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 619 removed outlier: 3.971A pdb=" N SER A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.983A pdb=" N LEU A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 704 removed outlier: 3.812A pdb=" N MET A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 738 removed outlier: 4.045A pdb=" N ARG A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 743 Processing helix chain 'A' and resid 747 through 777 removed outlier: 3.805A pdb=" N GLU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 11 Processing helix chain 'Y' and resid 11 through 31 removed outlier: 3.503A pdb=" N ARG Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 46 removed outlier: 3.967A pdb=" N LYS Y 45 " --> pdb=" O ASP Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 89 removed outlier: 3.944A pdb=" N MET Y 89 " --> pdb=" O GLN Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 102 removed outlier: 3.507A pdb=" N ALA Y 96 " --> pdb=" O VAL Y 92 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY Y 102 " --> pdb=" O TRP Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 137 Processing helix chain 'Y' and resid 145 through 174 Processing helix chain 'Y' and resid 177 through 202 Proline residue: Y 192 - end of helix removed outlier: 3.680A pdb=" N THR Y 202 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 214 through 236 Processing helix chain 'Y' and resid 271 through 292 removed outlier: 3.904A pdb=" N ILE Y 275 " --> pdb=" O VAL Y 271 " (cutoff:3.500A) Proline residue: Y 284 - end of helix Processing helix chain 'Y' and resid 295 through 304 Processing helix chain 'Y' and resid 308 through 331 Processing helix chain 'Y' and resid 332 through 343 removed outlier: 3.711A pdb=" N GLN Y 343 " --> pdb=" O ASN Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 353 through 380 removed outlier: 4.059A pdb=" N GLN Y 357 " --> pdb=" O GLY Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 380 through 390 removed outlier: 3.628A pdb=" N PHE Y 384 " --> pdb=" O VAL Y 380 " (cutoff:3.500A) Processing helix chain 'Y' and resid 400 through 423 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 22 through 59 Processing helix chain 'B' and resid 3 through 20 Processing helix chain 'B' and resid 36 through 43 Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.194A pdb=" N ALA A 98 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 97 " --> pdb=" O VAL A 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 226 removed outlier: 6.766A pdb=" N LEU A 221 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A 354 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A 223 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 253 Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 308 removed outlier: 4.181A pdb=" N ILE A 315 " --> pdb=" O MET A 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 402 removed outlier: 5.883A pdb=" N LEU A 406 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 400 through 402 removed outlier: 3.608A pdb=" N TYR A 538 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 433 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 238 through 242 638 hydrogen bonds defined for protein. 1884 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: 3.22 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2615 1.33 - 1.45: 2081 1.45 - 1.58: 5586 1.58 - 1.70: 3 1.70 - 1.82: 97 Bond restraints: 10382 Sorted by residual: bond pdb=" F1 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.767 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.11e+02 bond pdb=" F3 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.763 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" CB VAL A 209 " pdb=" CG2 VAL A 209 " ideal model delta sigma weight residual 1.521 1.393 0.128 3.30e-02 9.18e+02 1.50e+01 bond pdb=" C MET A 79 " pdb=" N PHE A 80 " ideal model delta sigma weight residual 1.331 1.263 0.068 2.07e-02 2.33e+03 1.09e+01 ... (remaining 10377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 13457 2.56 - 5.13: 487 5.13 - 7.69: 62 7.69 - 10.25: 13 10.25 - 12.82: 5 Bond angle restraints: 14024 Sorted by residual: angle pdb=" C ASN Y 66 " pdb=" CA ASN Y 66 " pdb=" CB ASN Y 66 " ideal model delta sigma weight residual 116.63 110.17 6.46 1.16e+00 7.43e-01 3.10e+01 angle pdb=" N LEU Y 64 " pdb=" CA LEU Y 64 " pdb=" C LEU Y 64 " ideal model delta sigma weight residual 112.12 105.51 6.61 1.34e+00 5.57e-01 2.43e+01 angle pdb=" C ALA Y 389 " pdb=" N ASN Y 390 " pdb=" CA ASN Y 390 " ideal model delta sigma weight residual 122.46 129.31 -6.85 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N VAL B 18 " pdb=" CA VAL B 18 " pdb=" C VAL B 18 " ideal model delta sigma weight residual 110.72 115.36 -4.64 1.01e+00 9.80e-01 2.11e+01 angle pdb=" N VAL Y 39 " pdb=" CA VAL Y 39 " pdb=" C VAL Y 39 " ideal model delta sigma weight residual 113.42 108.32 5.10 1.17e+00 7.31e-01 1.90e+01 ... (remaining 14019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.87: 5868 27.87 - 55.74: 372 55.74 - 83.62: 18 83.62 - 111.49: 0 111.49 - 139.36: 2 Dihedral angle restraints: 6260 sinusoidal: 2555 harmonic: 3705 Sorted by residual: dihedral pdb=" CB CYS Y 60 " pdb=" SG CYS Y 60 " pdb=" SG CYS B 26 " pdb=" CB CYS B 26 " ideal model delta sinusoidal sigma weight residual 93.00 169.64 -76.64 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" C5' ADP A1003 " pdb=" O5' ADP A1003 " pdb=" PA ADP A1003 " pdb=" O2A ADP A1003 " ideal model delta sinusoidal sigma weight residual 300.00 160.64 139.36 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PB ADP A1003 " pdb=" PA ADP A1003 " ideal model delta sinusoidal sigma weight residual 300.00 167.43 132.57 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 6257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1224 0.072 - 0.143: 331 0.143 - 0.215: 50 0.215 - 0.287: 5 0.287 - 0.359: 5 Chirality restraints: 1615 Sorted by residual: chirality pdb=" CB ILE A 738 " pdb=" CA ILE A 738 " pdb=" CG1 ILE A 738 " pdb=" CG2 ILE A 738 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB VAL Y 421 " pdb=" CA VAL Y 421 " pdb=" CG1 VAL Y 421 " pdb=" CG2 VAL Y 421 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB VAL A 209 " pdb=" CA VAL A 209 " pdb=" CG1 VAL A 209 " pdb=" CG2 VAL A 209 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 1612 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 63 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C VAL A 63 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL A 63 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU A 64 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 74 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ARG A 74 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG A 74 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG A 75 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 73 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C SER A 73 " -0.056 2.00e-02 2.50e+03 pdb=" O SER A 73 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 74 " 0.019 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 7 2.29 - 2.94: 4340 2.94 - 3.59: 14702 3.59 - 4.25: 22922 4.25 - 4.90: 40403 Nonbonded interactions: 82374 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb="BE BEF A1002 " model vdw 1.632 1.550 nonbonded pdb="MG MG A1001 " pdb=" F2 BEF A1002 " model vdw 1.940 2.120 nonbonded pdb="MG MG A1001 " pdb=" F3 BEF A1002 " model vdw 1.973 2.120 nonbonded pdb=" OD1 ASP A 210 " pdb=" OG1 THR A 371 " model vdw 2.103 3.040 nonbonded pdb=" OG SER Y 279 " pdb=" CD2 LEU B 17 " model vdw 2.248 3.460 ... (remaining 82369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.017 0.899 10386 Z= 1.067 Angle : 1.128 12.816 14026 Z= 0.618 Chirality : 0.068 0.359 1615 Planarity : 0.008 0.070 1784 Dihedral : 16.622 139.362 3871 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.73 % Allowed : 20.02 % Favored : 79.25 % Cbeta Deviations : 0.08 % 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: -3.25 (0.19), residues: 1268 helix: -1.79 (0.15), residues: 802 sheet: -2.56 (0.51), residues: 84 loop : -2.45 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 21 HIS 0.008 0.003 HIS A 739 PHE 0.024 0.003 PHE A 361 TYR 0.025 0.003 TYR A 743 ARG 0.012 0.001 ARG A 489 Details of bonding type rmsd hydrogen bonds : bond 0.15771 ( 636) hydrogen bonds : angle 6.75928 ( 1884) SS BOND : bond 0.00605 ( 1) SS BOND : angle 0.80162 ( 2) covalent geometry : bond 0.01429 (10382) covalent geometry : angle 1.12809 (14024) Misc. bond : bond 0.51905 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7646 (mtpp) REVERT: A 193 LYS cc_start: 0.8212 (tttt) cc_final: 0.7864 (ttmt) REVERT: A 255 LYS cc_start: 0.8579 (mptp) cc_final: 0.8295 (mmtm) REVERT: A 297 HIS cc_start: 0.8602 (OUTLIER) cc_final: 0.7985 (m90) REVERT: A 378 GLU cc_start: 0.7850 (tt0) cc_final: 0.7559 (tt0) REVERT: A 447 LYS cc_start: 0.8195 (pttp) cc_final: 0.7674 (ptpt) REVERT: A 469 GLN cc_start: 0.7496 (mt0) cc_final: 0.7204 (mt0) REVERT: A 557 MET cc_start: 0.5816 (mtt) cc_final: 0.5583 (mmm) REVERT: A 576 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7346 (mmt90) REVERT: A 604 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7594 (ttt180) REVERT: A 612 LYS cc_start: 0.8539 (tptp) cc_final: 0.8335 (tttm) REVERT: A 619 ASP cc_start: 0.8064 (p0) cc_final: 0.7851 (p0) REVERT: A 774 PHE cc_start: 0.8748 (m-10) cc_final: 0.8524 (m-80) REVERT: Y 94 LYS cc_start: 0.5180 (ttmt) cc_final: 0.4817 (tptt) REVERT: Y 164 MET cc_start: 0.6759 (mtp) cc_final: 0.6511 (mtp) REVERT: Y 312 MET cc_start: 0.8006 (ttp) cc_final: 0.7700 (ttm) REVERT: E 51 ILE cc_start: 0.8793 (mt) cc_final: 0.8577 (mm) outliers start: 8 outliers final: 3 residues processed: 201 average time/residue: 0.2812 time to fit residues: 75.6070 Evaluate side-chains 158 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 364 TYR Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 287 ASN A 291 ASN A 297 HIS A 301 GLN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN A 464 HIS A 529 GLN A 582 GLN A 736 GLN A 739 HIS A 753 GLN Y 134 ASN Y 267 ASN Y 355 ASN Y 387 ASN Y 419 GLN B 42 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.115930 restraints weight = 11871.389| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.78 r_work: 0.2993 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10386 Z= 0.169 Angle : 0.656 13.341 14026 Z= 0.346 Chirality : 0.043 0.172 1615 Planarity : 0.005 0.054 1784 Dihedral : 7.970 131.889 1410 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.00 % Allowed : 19.75 % Favored : 77.25 % 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: -0.93 (0.23), residues: 1268 helix: 0.18 (0.17), residues: 808 sheet: -1.79 (0.53), residues: 91 loop : -1.90 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Y 98 HIS 0.019 0.002 HIS B 67 PHE 0.048 0.002 PHE B 44 TYR 0.015 0.002 TYR A 250 ARG 0.004 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.06159 ( 636) hydrogen bonds : angle 5.07853 ( 1884) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.13470 ( 2) covalent geometry : bond 0.00357 (10382) covalent geometry : angle 0.65575 (14024) Misc. bond : bond 0.00275 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8033 (mmtm) cc_final: 0.7542 (mmmt) REVERT: A 193 LYS cc_start: 0.8383 (tttt) cc_final: 0.7917 (ttmt) REVERT: A 255 LYS cc_start: 0.8400 (mptp) cc_final: 0.8126 (mmtp) REVERT: A 297 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8275 (m-70) REVERT: A 447 LYS cc_start: 0.8330 (pttp) cc_final: 0.7776 (ptpt) REVERT: A 458 VAL cc_start: 0.9077 (p) cc_final: 0.8864 (t) REVERT: A 511 GLU cc_start: 0.8006 (pt0) cc_final: 0.7754 (pt0) REVERT: A 557 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5361 (mmm) REVERT: A 565 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 576 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7783 (mmt90) REVERT: A 604 ARG cc_start: 0.8388 (ttp80) cc_final: 0.7319 (ttt180) REVERT: A 612 LYS cc_start: 0.8632 (tptp) cc_final: 0.8212 (tttm) REVERT: A 774 PHE cc_start: 0.8681 (m-10) cc_final: 0.8441 (m-80) REVERT: Y 9 MET cc_start: 0.2959 (OUTLIER) cc_final: 0.2408 (ptt) REVERT: Y 94 LYS cc_start: 0.5485 (ttmt) cc_final: 0.4702 (tptt) REVERT: Y 98 TRP cc_start: 0.5908 (m-10) cc_final: 0.5354 (m-10) REVERT: Y 168 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6789 (tm-30) REVERT: Y 312 MET cc_start: 0.7826 (ttp) cc_final: 0.7541 (ttm) REVERT: Y 342 LYS cc_start: 0.7779 (ttpt) cc_final: 0.7408 (ttmm) REVERT: E 51 ILE cc_start: 0.8663 (mt) cc_final: 0.8374 (mm) outliers start: 33 outliers final: 16 residues processed: 182 average time/residue: 0.2362 time to fit residues: 60.1342 Evaluate side-chains 168 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 383 ASN ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN Y 101 GLN Y 308 HIS Y 396 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.117513 restraints weight = 12085.329| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.74 r_work: 0.3027 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10386 Z= 0.146 Angle : 0.593 11.066 14026 Z= 0.310 Chirality : 0.042 0.169 1615 Planarity : 0.004 0.054 1784 Dihedral : 7.178 120.311 1408 Min Nonbonded Distance : 1.274 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.55 % Allowed : 19.29 % Favored : 77.16 % 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: 0.16 (0.24), residues: 1268 helix: 1.09 (0.18), residues: 810 sheet: -1.56 (0.53), residues: 91 loop : -1.61 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 299 HIS 0.010 0.001 HIS B 67 PHE 0.024 0.001 PHE B 44 TYR 0.015 0.001 TYR B 66 ARG 0.005 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.05464 ( 636) hydrogen bonds : angle 4.64514 ( 1884) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.10478 ( 2) covalent geometry : bond 0.00314 (10382) covalent geometry : angle 0.59281 (14024) Misc. bond : bond 0.00179 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7100 (mtpp) REVERT: A 193 LYS cc_start: 0.8421 (tttt) cc_final: 0.7972 (ttmt) REVERT: A 255 LYS cc_start: 0.8410 (mptp) cc_final: 0.8169 (mmtp) REVERT: A 297 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8309 (m-70) REVERT: A 403 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7417 (mtt-85) REVERT: A 447 LYS cc_start: 0.8300 (pttp) cc_final: 0.7703 (ptpt) REVERT: A 557 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.5295 (mmm) REVERT: A 576 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7760 (mmt90) REVERT: A 604 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8186 (tmm-80) REVERT: A 612 LYS cc_start: 0.8648 (tptp) cc_final: 0.8244 (tttm) REVERT: A 774 PHE cc_start: 0.8721 (m-10) cc_final: 0.8506 (m-80) REVERT: Y 9 MET cc_start: 0.2837 (OUTLIER) cc_final: 0.2255 (ptt) REVERT: Y 94 LYS cc_start: 0.5437 (ttmt) cc_final: 0.4658 (tptt) REVERT: Y 98 TRP cc_start: 0.5864 (m-10) cc_final: 0.5555 (m-10) REVERT: Y 130 TYR cc_start: 0.7712 (t80) cc_final: 0.7174 (t80) REVERT: Y 168 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6767 (tm-30) REVERT: Y 312 MET cc_start: 0.7721 (ttp) cc_final: 0.7442 (ttm) REVERT: Y 342 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7440 (ttmm) REVERT: E 17 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8119 (mmtt) REVERT: B 43 MET cc_start: 0.7271 (ptm) cc_final: 0.7035 (ptt) outliers start: 39 outliers final: 22 residues processed: 187 average time/residue: 0.3094 time to fit residues: 79.4329 Evaluate side-chains 177 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 112 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 98 optimal weight: 0.2980 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.156951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121200 restraints weight = 11889.773| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.80 r_work: 0.3053 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10386 Z= 0.128 Angle : 0.564 9.830 14026 Z= 0.294 Chirality : 0.041 0.165 1615 Planarity : 0.004 0.053 1784 Dihedral : 6.891 113.052 1408 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.64 % Allowed : 21.29 % Favored : 76.07 % 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: 0.65 (0.24), residues: 1268 helix: 1.53 (0.18), residues: 809 sheet: -1.48 (0.53), residues: 91 loop : -1.54 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 299 HIS 0.006 0.001 HIS B 67 PHE 0.019 0.001 PHE B 44 TYR 0.011 0.001 TYR Y 306 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 636) hydrogen bonds : angle 4.46755 ( 1884) SS BOND : bond 0.00052 ( 1) SS BOND : angle 0.05263 ( 2) covalent geometry : bond 0.00261 (10382) covalent geometry : angle 0.56445 (14024) Misc. bond : bond 0.00124 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7381 (mmmt) REVERT: A 193 LYS cc_start: 0.8465 (tttt) cc_final: 0.8047 (ttmt) REVERT: A 297 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8283 (m-70) REVERT: A 403 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7442 (mtt-85) REVERT: A 447 LYS cc_start: 0.8261 (pttp) cc_final: 0.7730 (ptpt) REVERT: A 457 GLN cc_start: 0.8469 (mt0) cc_final: 0.8198 (mm-40) REVERT: A 473 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 555 MET cc_start: 0.4794 (mmt) cc_final: 0.4338 (tpt) REVERT: A 557 MET cc_start: 0.5613 (OUTLIER) cc_final: 0.5219 (mmm) REVERT: A 576 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7807 (mmt90) REVERT: A 600 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6640 (t70) REVERT: A 604 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8159 (tmm-80) REVERT: A 612 LYS cc_start: 0.8697 (tptp) cc_final: 0.8358 (tttm) REVERT: A 774 PHE cc_start: 0.8753 (m-10) cc_final: 0.8546 (m-80) REVERT: Y 9 MET cc_start: 0.2868 (OUTLIER) cc_final: 0.2227 (ptt) REVERT: Y 94 LYS cc_start: 0.5434 (ttmt) cc_final: 0.4647 (tptp) REVERT: Y 98 TRP cc_start: 0.5882 (m-10) cc_final: 0.5616 (m-10) REVERT: Y 124 GLN cc_start: 0.7941 (mm110) cc_final: 0.7228 (tp40) REVERT: Y 130 TYR cc_start: 0.7625 (t80) cc_final: 0.7134 (t80) REVERT: Y 168 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6889 (tm-30) REVERT: Y 312 MET cc_start: 0.7796 (ttp) cc_final: 0.7523 (ttm) REVERT: E 17 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8059 (mmtt) outliers start: 29 outliers final: 18 residues processed: 182 average time/residue: 0.2692 time to fit residues: 67.4519 Evaluate side-chains 174 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.164995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.139549 restraints weight = 11639.604| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.07 r_work: 0.3121 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10386 Z= 0.150 Angle : 0.574 10.059 14026 Z= 0.299 Chirality : 0.041 0.161 1615 Planarity : 0.004 0.052 1784 Dihedral : 6.882 115.752 1408 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.64 % Allowed : 20.66 % Favored : 75.71 % 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: 0.85 (0.24), residues: 1268 helix: 1.71 (0.18), residues: 807 sheet: -1.47 (0.53), residues: 91 loop : -1.49 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 299 HIS 0.004 0.001 HIS B 67 PHE 0.043 0.001 PHE B 44 TYR 0.018 0.001 TYR B 66 ARG 0.005 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 636) hydrogen bonds : angle 4.42996 ( 1884) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.07544 ( 2) covalent geometry : bond 0.00331 (10382) covalent geometry : angle 0.57425 (14024) Misc. bond : bond 0.00188 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8138 (mmtm) cc_final: 0.7696 (mmmt) REVERT: A 193 LYS cc_start: 0.8427 (tttt) cc_final: 0.8006 (ttpp) REVERT: A 297 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8312 (m-70) REVERT: A 447 LYS cc_start: 0.8237 (pttp) cc_final: 0.7829 (ptpt) REVERT: A 557 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5265 (mmm) REVERT: A 576 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7701 (mmt90) REVERT: A 604 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8176 (tmm-80) REVERT: A 774 PHE cc_start: 0.8797 (m-10) cc_final: 0.8567 (m-80) REVERT: Y 9 MET cc_start: 0.2863 (OUTLIER) cc_final: 0.2216 (ptt) REVERT: Y 94 LYS cc_start: 0.5566 (ttmt) cc_final: 0.4817 (tptp) REVERT: Y 98 TRP cc_start: 0.5998 (m-10) cc_final: 0.5795 (m-10) REVERT: Y 124 GLN cc_start: 0.7777 (mm110) cc_final: 0.7095 (tp40) REVERT: Y 130 TYR cc_start: 0.7543 (t80) cc_final: 0.7119 (t80) REVERT: Y 180 SER cc_start: 0.8648 (m) cc_final: 0.8299 (p) REVERT: Y 312 MET cc_start: 0.7921 (ttp) cc_final: 0.7642 (ttm) REVERT: E 17 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8173 (mmtt) outliers start: 40 outliers final: 28 residues processed: 179 average time/residue: 0.2322 time to fit residues: 58.6253 Evaluate side-chains 182 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.156006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.120194 restraints weight = 12007.945| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.69 r_work: 0.3037 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10386 Z= 0.142 Angle : 0.570 9.724 14026 Z= 0.295 Chirality : 0.041 0.148 1615 Planarity : 0.004 0.053 1784 Dihedral : 6.796 114.104 1408 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.18 % Allowed : 21.38 % Favored : 75.43 % 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: 1.04 (0.24), residues: 1268 helix: 1.83 (0.18), residues: 808 sheet: -1.33 (0.53), residues: 93 loop : -1.35 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 299 HIS 0.004 0.001 HIS B 67 PHE 0.037 0.001 PHE B 44 TYR 0.017 0.001 TYR B 66 ARG 0.006 0.000 ARG Y 15 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 636) hydrogen bonds : angle 4.37030 ( 1884) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.09665 ( 2) covalent geometry : bond 0.00313 (10382) covalent geometry : angle 0.56991 (14024) Misc. bond : bond 0.00165 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7861 (mmtm) cc_final: 0.7417 (mmmt) REVERT: A 193 LYS cc_start: 0.8515 (tttt) cc_final: 0.8009 (ttpp) REVERT: A 297 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8331 (m-70) REVERT: A 447 LYS cc_start: 0.8176 (pttp) cc_final: 0.7614 (ptpt) REVERT: A 457 GLN cc_start: 0.8571 (mt0) cc_final: 0.8296 (mm110) REVERT: A 473 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 557 MET cc_start: 0.5805 (OUTLIER) cc_final: 0.5174 (mmm) REVERT: A 576 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7795 (mmt90) REVERT: A 604 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8131 (tmm-80) REVERT: A 774 PHE cc_start: 0.8662 (m-10) cc_final: 0.8439 (m-80) REVERT: Y 9 MET cc_start: 0.2708 (OUTLIER) cc_final: 0.2108 (ptt) REVERT: Y 15 ARG cc_start: 0.6700 (ttp80) cc_final: 0.6211 (ttm110) REVERT: Y 94 LYS cc_start: 0.5272 (ttmt) cc_final: 0.4498 (tptt) REVERT: Y 98 TRP cc_start: 0.5815 (m-10) cc_final: 0.5562 (m-10) REVERT: Y 124 GLN cc_start: 0.7802 (mm110) cc_final: 0.7114 (tp40) REVERT: Y 130 TYR cc_start: 0.7631 (t80) cc_final: 0.7228 (t80) REVERT: Y 168 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6812 (tm-30) REVERT: Y 180 SER cc_start: 0.8557 (m) cc_final: 0.8155 (p) REVERT: Y 312 MET cc_start: 0.7723 (ttp) cc_final: 0.7441 (ttm) REVERT: E 17 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8089 (mmtt) outliers start: 35 outliers final: 27 residues processed: 179 average time/residue: 0.2856 time to fit residues: 72.8161 Evaluate side-chains 180 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 68 SER Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 17 LYS Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.118307 restraints weight = 12124.665| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.72 r_work: 0.3029 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10386 Z= 0.146 Angle : 0.567 9.699 14026 Z= 0.293 Chirality : 0.041 0.149 1615 Planarity : 0.004 0.052 1784 Dihedral : 6.787 115.009 1408 Min Nonbonded Distance : 1.252 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.55 % Allowed : 21.57 % Favored : 74.89 % 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: 1.14 (0.24), residues: 1268 helix: 1.89 (0.18), residues: 807 sheet: -1.20 (0.54), residues: 93 loop : -1.31 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 299 HIS 0.003 0.001 HIS B 67 PHE 0.026 0.001 PHE B 44 TYR 0.025 0.001 TYR A 665 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 636) hydrogen bonds : angle 4.35098 ( 1884) SS BOND : bond 0.00050 ( 1) SS BOND : angle 0.11535 ( 2) covalent geometry : bond 0.00324 (10382) covalent geometry : angle 0.56751 (14024) Misc. bond : bond 0.00173 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7403 (mmmt) REVERT: A 193 LYS cc_start: 0.8536 (tttt) cc_final: 0.8152 (ttpt) REVERT: A 207 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8048 (t0) REVERT: A 297 HIS cc_start: 0.8825 (OUTLIER) cc_final: 0.8370 (m-70) REVERT: A 370 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8205 (ptp) REVERT: A 447 LYS cc_start: 0.8177 (pttp) cc_final: 0.7620 (ptpt) REVERT: A 457 GLN cc_start: 0.8568 (mt0) cc_final: 0.8289 (mm110) REVERT: A 473 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7619 (mt-10) REVERT: A 555 MET cc_start: 0.5847 (tpp) cc_final: 0.5636 (tpt) REVERT: A 557 MET cc_start: 0.5793 (OUTLIER) cc_final: 0.5190 (mmm) REVERT: A 576 ARG cc_start: 0.8103 (tpp80) cc_final: 0.7762 (mmt90) REVERT: A 604 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8002 (tmm-80) REVERT: A 608 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8128 (mt-10) REVERT: Y 9 MET cc_start: 0.2652 (OUTLIER) cc_final: 0.2109 (ptt) REVERT: Y 15 ARG cc_start: 0.6641 (ttp80) cc_final: 0.6136 (ttm110) REVERT: Y 74 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8473 (t) REVERT: Y 94 LYS cc_start: 0.5334 (ttmt) cc_final: 0.4506 (tptt) REVERT: Y 98 TRP cc_start: 0.5640 (m-10) cc_final: 0.5369 (m-10) REVERT: Y 124 GLN cc_start: 0.7834 (mm110) cc_final: 0.7141 (tp40) REVERT: Y 130 TYR cc_start: 0.7656 (t80) cc_final: 0.7296 (t80) REVERT: Y 168 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6833 (tm-30) REVERT: Y 180 SER cc_start: 0.8521 (m) cc_final: 0.8133 (p) REVERT: Y 302 ARG cc_start: 0.6788 (ttp-110) cc_final: 0.6512 (ptm160) REVERT: Y 312 MET cc_start: 0.7726 (ttp) cc_final: 0.7424 (ttm) outliers start: 39 outliers final: 28 residues processed: 179 average time/residue: 0.2605 time to fit residues: 65.4668 Evaluate side-chains 186 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 68 SER Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.155437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118238 restraints weight = 12013.859| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.75 r_work: 0.3032 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10386 Z= 0.141 Angle : 0.568 9.433 14026 Z= 0.292 Chirality : 0.041 0.144 1615 Planarity : 0.004 0.052 1784 Dihedral : 6.750 114.670 1408 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.46 % Allowed : 21.47 % Favored : 75.07 % 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: 1.22 (0.24), residues: 1268 helix: 1.96 (0.18), residues: 802 sheet: -1.16 (0.54), residues: 93 loop : -1.24 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 299 HIS 0.003 0.001 HIS B 67 PHE 0.027 0.001 PHE B 44 TYR 0.022 0.001 TYR A 665 ARG 0.006 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.05017 ( 636) hydrogen bonds : angle 4.31829 ( 1884) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.13787 ( 2) covalent geometry : bond 0.00311 (10382) covalent geometry : angle 0.56843 (14024) Misc. bond : bond 0.00169 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7186 (mttt) REVERT: A 193 LYS cc_start: 0.8552 (tttt) cc_final: 0.8180 (ttpt) REVERT: A 207 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8028 (t0) REVERT: A 297 HIS cc_start: 0.8829 (OUTLIER) cc_final: 0.8385 (m-70) REVERT: A 370 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8205 (ptp) REVERT: A 447 LYS cc_start: 0.8239 (pttp) cc_final: 0.7891 (pttt) REVERT: A 457 GLN cc_start: 0.8587 (mt0) cc_final: 0.8316 (mm110) REVERT: A 473 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 555 MET cc_start: 0.5838 (tpp) cc_final: 0.5607 (tpt) REVERT: A 557 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5195 (mmm) REVERT: A 576 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7822 (mmt90) REVERT: A 604 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8005 (tmm-80) REVERT: A 608 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8106 (mt-10) REVERT: Y 9 MET cc_start: 0.2762 (OUTLIER) cc_final: 0.2160 (ptt) REVERT: Y 15 ARG cc_start: 0.6651 (ttp80) cc_final: 0.6159 (ttm110) REVERT: Y 74 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8416 (t) REVERT: Y 94 LYS cc_start: 0.5261 (ttmt) cc_final: 0.4473 (tptt) REVERT: Y 98 TRP cc_start: 0.5654 (m-10) cc_final: 0.5388 (m-10) REVERT: Y 130 TYR cc_start: 0.7632 (t80) cc_final: 0.7271 (t80) REVERT: Y 168 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6866 (tm-30) REVERT: Y 302 ARG cc_start: 0.6782 (ttp-110) cc_final: 0.6506 (ptm160) REVERT: Y 312 MET cc_start: 0.7732 (ttp) cc_final: 0.7411 (ttm) outliers start: 38 outliers final: 31 residues processed: 183 average time/residue: 0.2582 time to fit residues: 66.6656 Evaluate side-chains 189 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 68 SER Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 80 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 81 optimal weight: 0.0070 chunk 94 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.154035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.116722 restraints weight = 12053.482| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.74 r_work: 0.3013 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10386 Z= 0.167 Angle : 0.589 9.774 14026 Z= 0.303 Chirality : 0.042 0.150 1615 Planarity : 0.004 0.051 1784 Dihedral : 6.833 116.514 1408 Min Nonbonded Distance : 1.238 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.55 % Allowed : 21.75 % Favored : 74.70 % 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: 1.15 (0.24), residues: 1268 helix: 1.90 (0.18), residues: 804 sheet: -1.18 (0.53), residues: 93 loop : -1.27 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 299 HIS 0.003 0.001 HIS B 67 PHE 0.028 0.001 PHE B 44 TYR 0.022 0.002 TYR A 665 ARG 0.007 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.05295 ( 636) hydrogen bonds : angle 4.36410 ( 1884) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.12155 ( 2) covalent geometry : bond 0.00380 (10382) covalent geometry : angle 0.58946 (14024) Misc. bond : bond 0.00213 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7248 (mttt) REVERT: A 193 LYS cc_start: 0.8652 (tttt) cc_final: 0.8291 (ttpt) REVERT: A 207 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8059 (t0) REVERT: A 297 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8417 (m-70) REVERT: A 370 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8267 (ptp) REVERT: A 447 LYS cc_start: 0.8252 (pttp) cc_final: 0.7916 (pttt) REVERT: A 457 GLN cc_start: 0.8605 (mt0) cc_final: 0.8319 (mm110) REVERT: A 473 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 555 MET cc_start: 0.5885 (tpp) cc_final: 0.5643 (tpt) REVERT: A 557 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5237 (mmm) REVERT: A 576 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7821 (mmt90) REVERT: A 604 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8029 (tmm-80) REVERT: A 608 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8134 (mt-10) REVERT: Y 9 MET cc_start: 0.2775 (OUTLIER) cc_final: 0.2193 (ptt) REVERT: Y 15 ARG cc_start: 0.6689 (ttp80) cc_final: 0.6199 (ttm110) REVERT: Y 94 LYS cc_start: 0.5433 (ttmt) cc_final: 0.4562 (tptt) REVERT: Y 98 TRP cc_start: 0.5669 (m-10) cc_final: 0.5379 (m-10) REVERT: Y 130 TYR cc_start: 0.7660 (t80) cc_final: 0.7285 (t80) REVERT: Y 168 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6903 (tm-30) REVERT: Y 302 ARG cc_start: 0.6781 (ttp-110) cc_final: 0.6500 (ptm160) REVERT: Y 312 MET cc_start: 0.7761 (ttp) cc_final: 0.7476 (ttm) REVERT: E 51 ILE cc_start: 0.8693 (mt) cc_final: 0.8413 (mm) outliers start: 39 outliers final: 30 residues processed: 178 average time/residue: 0.2444 time to fit residues: 60.3700 Evaluate side-chains 184 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 68 SER Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.0020 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.154532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.117296 restraints weight = 11974.281| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.73 r_work: 0.3016 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10386 Z= 0.160 Angle : 0.586 10.175 14026 Z= 0.302 Chirality : 0.042 0.148 1615 Planarity : 0.004 0.052 1784 Dihedral : 6.831 116.577 1408 Min Nonbonded Distance : 1.235 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.46 % Allowed : 21.57 % Favored : 74.98 % 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: 1.18 (0.24), residues: 1268 helix: 1.92 (0.18), residues: 803 sheet: -1.12 (0.54), residues: 93 loop : -1.27 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 299 HIS 0.003 0.001 HIS B 67 PHE 0.027 0.001 PHE B 44 TYR 0.021 0.002 TYR A 665 ARG 0.007 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 636) hydrogen bonds : angle 4.34916 ( 1884) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.16732 ( 2) covalent geometry : bond 0.00362 (10382) covalent geometry : angle 0.58621 (14024) Misc. bond : bond 0.00198 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7201 (mttt) REVERT: A 193 LYS cc_start: 0.8642 (tttt) cc_final: 0.8272 (ttpt) REVERT: A 207 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8020 (t0) REVERT: A 266 MET cc_start: 0.8348 (mtm) cc_final: 0.8142 (mtm) REVERT: A 297 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8461 (m-70) REVERT: A 370 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8275 (ptp) REVERT: A 447 LYS cc_start: 0.8229 (pttp) cc_final: 0.7891 (pttt) REVERT: A 473 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 555 MET cc_start: 0.5961 (tpp) cc_final: 0.5700 (tpt) REVERT: A 557 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5221 (mmm) REVERT: A 576 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7800 (mmt90) REVERT: A 604 ARG cc_start: 0.8432 (ttp80) cc_final: 0.8006 (tmm-80) REVERT: A 608 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8096 (mt-10) REVERT: Y 9 MET cc_start: 0.2685 (OUTLIER) cc_final: 0.2103 (ptt) REVERT: Y 15 ARG cc_start: 0.6633 (ttp80) cc_final: 0.6142 (ttm110) REVERT: Y 94 LYS cc_start: 0.5109 (ttmt) cc_final: 0.4354 (tptt) REVERT: Y 98 TRP cc_start: 0.5667 (m-10) cc_final: 0.5380 (m-10) REVERT: Y 130 TYR cc_start: 0.7675 (t80) cc_final: 0.7314 (t80) REVERT: Y 168 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6864 (tm-30) REVERT: Y 180 SER cc_start: 0.8564 (m) cc_final: 0.8154 (p) REVERT: Y 302 ARG cc_start: 0.6747 (ttp-110) cc_final: 0.6471 (ptm160) REVERT: Y 312 MET cc_start: 0.7705 (ttp) cc_final: 0.7423 (ttm) REVERT: E 51 ILE cc_start: 0.8696 (mt) cc_final: 0.8430 (mm) outliers start: 38 outliers final: 31 residues processed: 183 average time/residue: 0.2458 time to fit residues: 62.8327 Evaluate side-chains 186 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 68 SER Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 175 VAL Chi-restraints excluded: chain Y residue 227 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 336 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 111 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.156047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.119486 restraints weight = 11851.098| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.74 r_work: 0.3053 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10386 Z= 0.126 Angle : 0.562 8.650 14026 Z= 0.290 Chirality : 0.040 0.133 1615 Planarity : 0.004 0.051 1784 Dihedral : 6.633 111.302 1408 Min Nonbonded Distance : 1.304 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.91 % Allowed : 22.29 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1268 helix: 2.11 (0.18), residues: 799 sheet: -1.20 (0.51), residues: 102 loop : -1.23 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 299 HIS 0.003 0.000 HIS B 67 PHE 0.047 0.001 PHE B 44 TYR 0.020 0.001 TYR A 665 ARG 0.008 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 636) hydrogen bonds : angle 4.25303 ( 1884) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.05518 ( 2) covalent geometry : bond 0.00261 (10382) covalent geometry : angle 0.56183 (14024) Misc. bond : bond 0.00137 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6713.45 seconds wall clock time: 118 minutes 55.64 seconds (7135.64 seconds total)