Starting phenix.real_space_refine on Wed Sep 17 17:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9y_39085/09_2025/8y9y_39085.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9y_39085/09_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_39085/09_2025/8y9y_39085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9y_39085/09_2025/8y9y_39085.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9y_39085/09_2025/8y9y_39085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9y_39085/09_2025/8y9y_39085.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.32, per 1000 atoms: 0.23 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: 0.97 Conformation dependent library (CDL) restraints added in 309.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.63 Time building geometry restraints manager: 1.31 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.200 ------------------------------------------------------------------------------- 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 : 6.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (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 ARG 0.012 0.001 ARG A 489 TYR 0.025 0.003 TYR A 743 PHE 0.024 0.003 PHE A 361 TRP 0.012 0.002 TRP B 21 HIS 0.008 0.003 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.01429 (10382) covalent geometry : angle 1.12809 (14024) SS BOND : bond 0.00605 ( 1) SS BOND : angle 0.80162 ( 2) hydrogen bonds : bond 0.15771 ( 636) hydrogen bonds : angle 6.75928 ( 1884) 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 : 0.392 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: 0.1273 time to fit residues: 34.2825 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 : 0.389 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.154353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118506 restraints weight = 11896.298| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.85 r_work: 0.2977 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10386 Z= 0.180 Angle : 0.662 13.575 14026 Z= 0.351 Chirality : 0.043 0.157 1615 Planarity : 0.005 0.054 1784 Dihedral : 7.991 132.071 1410 Min Nonbonded Distance : 1.263 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.09 % Allowed : 19.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.23), residues: 1268 helix: 0.16 (0.17), residues: 808 sheet: -1.83 (0.54), residues: 86 loop : -1.91 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.015 0.002 TYR A 250 PHE 0.054 0.002 PHE B 44 TRP 0.008 0.002 TRP Y 98 HIS 0.019 0.002 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00383 (10382) covalent geometry : angle 0.66253 (14024) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.16955 ( 2) hydrogen bonds : bond 0.06220 ( 636) hydrogen bonds : angle 5.08484 ( 1884) Misc. bond : bond 0.00434 ( 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: 34 poor density : 156 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8106 (mmtm) cc_final: 0.7276 (mtpp) REVERT: A 193 LYS cc_start: 0.8407 (tttt) cc_final: 0.7963 (ttmt) REVERT: A 255 LYS cc_start: 0.8471 (mptp) cc_final: 0.8208 (mmtp) REVERT: A 297 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8327 (m-70) REVERT: A 447 LYS cc_start: 0.8369 (pttp) cc_final: 0.7831 (ptpt) REVERT: A 458 VAL cc_start: 0.9087 (p) cc_final: 0.8879 (t) REVERT: A 511 GLU cc_start: 0.8033 (pt0) cc_final: 0.7796 (pt0) REVERT: A 557 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5364 (mmm) REVERT: A 565 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: A 576 ARG cc_start: 0.8220 (tpp80) cc_final: 0.7830 (mmt90) REVERT: A 604 ARG cc_start: 0.8454 (ttp80) cc_final: 0.7450 (ttt180) REVERT: A 612 LYS cc_start: 0.8695 (tptp) cc_final: 0.8306 (tttm) REVERT: A 774 PHE cc_start: 0.8739 (m-10) cc_final: 0.8504 (m-80) REVERT: Y 9 MET cc_start: 0.3013 (OUTLIER) cc_final: 0.2421 (ptt) REVERT: Y 94 LYS cc_start: 0.5437 (ttmt) cc_final: 0.4799 (tptt) REVERT: Y 98 TRP cc_start: 0.5971 (m-10) cc_final: 0.5406 (m-10) REVERT: Y 168 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6873 (tm-30) REVERT: Y 312 MET cc_start: 0.7907 (ttp) cc_final: 0.7623 (ttm) REVERT: Y 342 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7476 (ttmm) REVERT: E 51 ILE cc_start: 0.8691 (mt) cc_final: 0.8392 (mm) outliers start: 34 outliers final: 17 residues processed: 182 average time/residue: 0.0991 time to fit residues: 25.4505 Evaluate side-chains 166 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 124 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 85 GLN Y 101 GLN Y 308 HIS Y 396 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.153300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116567 restraints weight = 12033.499| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.74 r_work: 0.3006 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10386 Z= 0.162 Angle : 0.607 11.462 14026 Z= 0.317 Chirality : 0.043 0.178 1615 Planarity : 0.004 0.054 1784 Dihedral : 7.320 123.536 1408 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.37 % Allowed : 19.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1268 helix: 1.00 (0.18), residues: 810 sheet: -1.62 (0.54), residues: 91 loop : -1.64 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 327 TYR 0.015 0.001 TYR B 66 PHE 0.027 0.001 PHE B 44 TRP 0.006 0.001 TRP Y 299 HIS 0.010 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00359 (10382) covalent geometry : angle 0.60714 (14024) SS BOND : bond 0.00062 ( 1) SS BOND : angle 0.09764 ( 2) hydrogen bonds : bond 0.05665 ( 636) hydrogen bonds : angle 4.70890 ( 1884) 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 197 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7882 (mmtm) cc_final: 0.7080 (mtpp) REVERT: A 193 LYS cc_start: 0.8463 (tttt) cc_final: 0.8023 (ttmt) REVERT: A 255 LYS cc_start: 0.8415 (mptp) cc_final: 0.8169 (mmtp) REVERT: A 297 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8356 (m-70) REVERT: A 447 LYS cc_start: 0.8312 (pttp) cc_final: 0.7718 (ptpt) REVERT: A 458 VAL cc_start: 0.9083 (p) cc_final: 0.8879 (t) REVERT: A 557 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.5342 (mmm) REVERT: A 565 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: A 576 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7784 (mmt90) REVERT: A 604 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8233 (tmm-80) REVERT: A 612 LYS cc_start: 0.8653 (tptp) cc_final: 0.8164 (tttm) REVERT: A 774 PHE cc_start: 0.8736 (m-10) cc_final: 0.8526 (m-80) REVERT: Y 9 MET cc_start: 0.2926 (OUTLIER) cc_final: 0.2288 (ptt) REVERT: Y 94 LYS cc_start: 0.5505 (ttmt) cc_final: 0.4741 (tptt) REVERT: Y 98 TRP cc_start: 0.5892 (m-10) cc_final: 0.5587 (m-10) REVERT: Y 130 TYR cc_start: 0.7707 (t80) cc_final: 0.7129 (t80) REVERT: Y 168 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6782 (tm-30) REVERT: Y 312 MET cc_start: 0.7746 (ttp) cc_final: 0.7457 (ttm) REVERT: Y 342 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7438 (ttmm) REVERT: E 17 LYS cc_start: 0.8261 (mttm) cc_final: 0.8035 (mmtt) REVERT: B 43 MET cc_start: 0.7260 (ptm) cc_final: 0.6967 (ptt) outliers start: 37 outliers final: 23 residues processed: 183 average time/residue: 0.1079 time to fit residues: 27.1291 Evaluate side-chains 175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 MET 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 610 ILE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 658 VAL 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 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 385 PHE 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 42 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116461 restraints weight = 12045.046| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.76 r_work: 0.3010 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2462 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= 0.157 Angle : 0.591 10.964 14026 Z= 0.308 Chirality : 0.042 0.171 1615 Planarity : 0.004 0.053 1784 Dihedral : 7.085 117.559 1408 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.28 % Allowed : 21.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.24), residues: 1268 helix: 1.40 (0.18), residues: 806 sheet: -1.56 (0.53), residues: 91 loop : -1.60 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.015 0.001 TYR B 66 PHE 0.021 0.001 PHE B 44 TRP 0.007 0.001 TRP Y 299 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00349 (10382) covalent geometry : angle 0.59084 (14024) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.08964 ( 2) hydrogen bonds : bond 0.05460 ( 636) hydrogen bonds : angle 4.59947 ( 1884) Misc. bond : bond 0.00184 ( 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 196 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7188 (mtpp) REVERT: A 193 LYS cc_start: 0.8473 (tttt) cc_final: 0.8046 (ttmt) REVERT: A 297 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8320 (m-70) REVERT: A 447 LYS cc_start: 0.8328 (pttp) cc_final: 0.7761 (ptpt) REVERT: A 557 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5026 (mmm) REVERT: A 576 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7772 (mmt90) REVERT: A 604 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8204 (tmm-80) REVERT: A 612 LYS cc_start: 0.8694 (tptp) cc_final: 0.8279 (tttm) REVERT: A 774 PHE cc_start: 0.8723 (m-10) cc_final: 0.8521 (m-80) REVERT: Y 9 MET cc_start: 0.2739 (OUTLIER) cc_final: 0.2127 (ptt) REVERT: Y 94 LYS cc_start: 0.5434 (ttmt) cc_final: 0.4620 (tptp) REVERT: Y 98 TRP cc_start: 0.5882 (m-10) cc_final: 0.5569 (m-10) REVERT: Y 124 GLN cc_start: 0.7894 (mm110) cc_final: 0.7052 (tp40) REVERT: Y 130 TYR cc_start: 0.7743 (t80) cc_final: 0.7184 (t80) REVERT: Y 312 MET cc_start: 0.7749 (ttp) cc_final: 0.7451 (ttm) REVERT: E 17 LYS cc_start: 0.8228 (mttm) cc_final: 0.7991 (mmtt) REVERT: B 43 MET cc_start: 0.7276 (ptm) cc_final: 0.6794 (ptt) outliers start: 36 outliers final: 26 residues processed: 183 average time/residue: 0.0995 time to fit residues: 25.4447 Evaluate side-chains 175 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 MET 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 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 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 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 22 VAL 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 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 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 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.154487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117370 restraints weight = 11978.988| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.80 r_work: 0.3015 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10386 Z= 0.147 Angle : 0.577 10.294 14026 Z= 0.300 Chirality : 0.041 0.165 1615 Planarity : 0.004 0.052 1784 Dihedral : 6.939 116.589 1408 Min Nonbonded Distance : 1.259 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.00 % Allowed : 22.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.24), residues: 1268 helix: 1.61 (0.18), residues: 807 sheet: -1.55 (0.53), residues: 91 loop : -1.49 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.013 0.001 TYR A 250 PHE 0.017 0.001 PHE B 44 TRP 0.007 0.001 TRP Y 299 HIS 0.005 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00324 (10382) covalent geometry : angle 0.57721 (14024) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.13418 ( 2) hydrogen bonds : bond 0.05236 ( 636) hydrogen bonds : angle 4.51641 ( 1884) Misc. bond : bond 0.00174 ( 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 191 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7362 (mmmt) REVERT: A 193 LYS cc_start: 0.8517 (tttt) cc_final: 0.8012 (ttpp) REVERT: A 297 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8345 (m-70) REVERT: A 447 LYS cc_start: 0.8319 (pttp) cc_final: 0.7751 (ptpt) REVERT: A 473 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 557 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5020 (mmm) REVERT: A 576 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7803 (mmt90) REVERT: A 600 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6653 (t70) REVERT: A 604 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8184 (tmm-80) REVERT: A 612 LYS cc_start: 0.8728 (tptp) cc_final: 0.8326 (tttm) REVERT: Y 9 MET cc_start: 0.2743 (OUTLIER) cc_final: 0.2094 (ptt) REVERT: Y 15 ARG cc_start: 0.6500 (ttp-110) cc_final: 0.6223 (ttp80) REVERT: Y 94 LYS cc_start: 0.5439 (ttmt) cc_final: 0.4630 (tptp) REVERT: Y 98 TRP cc_start: 0.5924 (m-10) cc_final: 0.5583 (m-10) REVERT: Y 124 GLN cc_start: 0.7862 (mm110) cc_final: 0.7133 (tp40) REVERT: Y 130 TYR cc_start: 0.7684 (t80) cc_final: 0.7201 (t80) REVERT: Y 168 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6890 (tm-30) REVERT: Y 180 SER cc_start: 0.8592 (m) cc_final: 0.8225 (p) REVERT: Y 312 MET cc_start: 0.7740 (ttp) cc_final: 0.7447 (ttm) REVERT: E 17 LYS cc_start: 0.8240 (mttm) cc_final: 0.7997 (mmtt) outliers start: 33 outliers final: 27 residues processed: 179 average time/residue: 0.1040 time to fit residues: 26.0486 Evaluate side-chains 184 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 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 600 ASP 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 Y residue 9 MET Chi-restraints excluded: chain Y residue 21 THR Chi-restraints excluded: chain Y residue 46 LEU 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 E residue 32 VAL Chi-restraints excluded: chain B residue 36 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 19 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 111 optimal weight: 0.0000 chunk 70 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.155925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.119033 restraints weight = 12057.136| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.79 r_work: 0.3035 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10386 Z= 0.133 Angle : 0.567 9.497 14026 Z= 0.294 Chirality : 0.041 0.138 1615 Planarity : 0.004 0.052 1784 Dihedral : 6.807 113.623 1408 Min Nonbonded Distance : 1.281 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.18 % Allowed : 22.38 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.24), residues: 1268 helix: 1.78 (0.18), residues: 808 sheet: -1.41 (0.53), residues: 91 loop : -1.37 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.018 0.001 TYR B 66 PHE 0.044 0.001 PHE B 44 TRP 0.008 0.001 TRP Y 299 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00284 (10382) covalent geometry : angle 0.56662 (14024) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.00929 ( 2) hydrogen bonds : bond 0.05000 ( 636) hydrogen bonds : angle 4.41523 ( 1884) Misc. bond : bond 0.00141 ( 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 194 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7855 (mmtm) cc_final: 0.7398 (mmmt) REVERT: A 193 LYS cc_start: 0.8534 (tttt) cc_final: 0.8015 (ttpp) REVERT: A 207 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8022 (t0) REVERT: A 297 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8324 (m-70) REVERT: A 447 LYS cc_start: 0.8200 (pttp) cc_final: 0.7629 (ptpt) REVERT: A 457 GLN cc_start: 0.8542 (mt0) cc_final: 0.8258 (mm110) REVERT: A 473 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 557 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5092 (mmm) REVERT: A 576 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7758 (mmt90) REVERT: A 600 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6616 (t70) REVERT: A 604 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7997 (tmm-80) REVERT: A 608 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8031 (mt-10) REVERT: Y 9 MET cc_start: 0.2661 (OUTLIER) cc_final: 0.2074 (ptt) REVERT: Y 15 ARG cc_start: 0.6476 (ttp-110) cc_final: 0.6200 (ttp80) REVERT: Y 94 LYS cc_start: 0.5453 (ttmt) cc_final: 0.4622 (tptt) REVERT: Y 98 TRP cc_start: 0.5953 (m-10) cc_final: 0.5645 (m-10) REVERT: Y 124 GLN cc_start: 0.7796 (mm110) cc_final: 0.7110 (tp40) REVERT: Y 130 TYR cc_start: 0.7652 (t80) cc_final: 0.7240 (t80) REVERT: Y 168 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6745 (tm-30) REVERT: Y 180 SER cc_start: 0.8531 (m) cc_final: 0.8130 (p) REVERT: Y 302 ARG cc_start: 0.6778 (ttp-110) cc_final: 0.6477 (ptm160) REVERT: Y 312 MET cc_start: 0.7681 (ttp) cc_final: 0.7397 (ttm) REVERT: E 17 LYS cc_start: 0.8173 (mttm) cc_final: 0.7936 (mmtt) outliers start: 35 outliers final: 24 residues processed: 184 average time/residue: 0.1070 time to fit residues: 27.4442 Evaluate side-chains 178 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 600 ASP 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 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 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 35 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.152311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.115047 restraints weight = 12002.784| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.74 r_work: 0.2985 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10386 Z= 0.201 Angle : 0.618 11.279 14026 Z= 0.319 Chirality : 0.043 0.158 1615 Planarity : 0.004 0.052 1784 Dihedral : 7.032 120.625 1408 Min Nonbonded Distance : 1.209 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.46 % Allowed : 22.20 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.24), residues: 1268 helix: 1.72 (0.18), residues: 804 sheet: -1.36 (0.53), residues: 91 loop : -1.33 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 327 TYR 0.019 0.002 TYR B 66 PHE 0.038 0.002 PHE B 44 TRP 0.007 0.001 TRP Y 299 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00471 (10382) covalent geometry : angle 0.61775 (14024) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.15165 ( 2) hydrogen bonds : bond 0.05666 ( 636) hydrogen bonds : angle 4.49744 ( 1884) Misc. bond : bond 0.00245 ( 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 193 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.392 Fit side-chains REVERT: A 54 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7318 (mtpp) REVERT: A 193 LYS cc_start: 0.8646 (tttt) cc_final: 0.8284 (ttpt) REVERT: A 207 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8074 (t0) REVERT: A 297 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8464 (m-70) REVERT: A 447 LYS cc_start: 0.8265 (pttp) cc_final: 0.7933 (pttt) REVERT: A 473 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 557 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.5205 (mmm) REVERT: A 576 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7819 (mmt90) REVERT: A 604 ARG cc_start: 0.8468 (ttp80) cc_final: 0.8057 (tmm-80) REVERT: A 608 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8117 (mt-10) REVERT: Y 9 MET cc_start: 0.2859 (OUTLIER) cc_final: 0.2409 (ptt) REVERT: Y 15 ARG cc_start: 0.6514 (ttp-110) cc_final: 0.6249 (ttp80) REVERT: Y 94 LYS cc_start: 0.5289 (ttmt) cc_final: 0.4478 (tptt) REVERT: Y 98 TRP cc_start: 0.5695 (m-10) cc_final: 0.5342 (m-10) REVERT: Y 130 TYR cc_start: 0.7680 (t80) cc_final: 0.7321 (t80) REVERT: Y 168 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6877 (tm-30) REVERT: Y 180 SER cc_start: 0.8571 (m) cc_final: 0.8172 (p) REVERT: Y 302 ARG cc_start: 0.6788 (ttp-110) cc_final: 0.6539 (ptm160) REVERT: Y 312 MET cc_start: 0.7730 (ttp) cc_final: 0.7414 (ttm) REVERT: E 17 LYS cc_start: 0.8298 (mttm) cc_final: 0.8052 (mmtt) outliers start: 38 outliers final: 28 residues processed: 182 average time/residue: 0.1187 time to fit residues: 29.5475 Evaluate side-chains 184 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 305 ASP 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 636 GLU Chi-restraints excluded: chain A residue 658 VAL 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 19 SER Chi-restraints excluded: chain E residue 32 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.153291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116391 restraints weight = 11894.089| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.79 r_work: 0.3010 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2860 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= 0.150 Angle : 0.579 9.881 14026 Z= 0.299 Chirality : 0.041 0.143 1615 Planarity : 0.004 0.053 1784 Dihedral : 6.883 115.748 1408 Min Nonbonded Distance : 1.234 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.09 % Allowed : 22.47 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.24), residues: 1268 helix: 1.85 (0.18), residues: 801 sheet: -1.27 (0.53), residues: 91 loop : -1.23 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.018 0.001 TYR B 66 PHE 0.031 0.001 PHE B 44 TRP 0.007 0.001 TRP Y 299 HIS 0.003 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00336 (10382) covalent geometry : angle 0.57895 (14024) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.12228 ( 2) hydrogen bonds : bond 0.05197 ( 636) hydrogen bonds : angle 4.41935 ( 1884) Misc. bond : bond 0.00173 ( 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 192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.423 Fit side-chains REVERT: A 54 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7412 (mmmt) REVERT: A 193 LYS cc_start: 0.8665 (tttt) cc_final: 0.8306 (ttpt) REVERT: A 207 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8031 (t0) REVERT: A 297 HIS cc_start: 0.8841 (OUTLIER) cc_final: 0.8391 (m-70) REVERT: A 370 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8288 (ptp) REVERT: A 447 LYS cc_start: 0.8221 (pttp) cc_final: 0.7885 (pttt) REVERT: A 457 GLN cc_start: 0.8611 (mt0) cc_final: 0.8335 (mm110) REVERT: A 473 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 557 MET cc_start: 0.5623 (OUTLIER) cc_final: 0.5190 (mmm) REVERT: A 576 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7783 (mmt90) REVERT: A 600 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6681 (t70) REVERT: A 604 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8057 (tmm-80) REVERT: A 608 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8094 (mt-10) REVERT: Y 9 MET cc_start: 0.2810 (OUTLIER) cc_final: 0.2237 (ptt) REVERT: Y 15 ARG cc_start: 0.6558 (ttp-110) cc_final: 0.5964 (ttm110) REVERT: Y 94 LYS cc_start: 0.5343 (ttmt) cc_final: 0.4503 (tptt) REVERT: Y 98 TRP cc_start: 0.5660 (m-10) cc_final: 0.5374 (m-10) REVERT: Y 130 TYR cc_start: 0.7683 (t80) cc_final: 0.7312 (t80) REVERT: Y 168 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6891 (tm-30) REVERT: Y 180 SER cc_start: 0.8594 (m) cc_final: 0.8184 (p) REVERT: Y 302 ARG cc_start: 0.6730 (ttp-110) cc_final: 0.6489 (ptm160) REVERT: Y 312 MET cc_start: 0.7758 (ttp) cc_final: 0.7461 (ttm) REVERT: Y 397 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5032 (tp) REVERT: E 17 LYS cc_start: 0.8225 (mttm) cc_final: 0.7984 (mmtt) outliers start: 34 outliers final: 25 residues processed: 181 average time/residue: 0.1135 time to fit residues: 28.3835 Evaluate side-chains 186 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 600 ASP 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 118 ILE Chi-restraints excluded: chain Y residue 135 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 Y residue 397 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 44 optimal weight: 0.0670 chunk 50 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.158825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125550 restraints weight = 11821.313| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.68 r_work: 0.3073 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10386 Z= 0.129 Angle : 0.555 8.409 14026 Z= 0.287 Chirality : 0.040 0.155 1615 Planarity : 0.004 0.053 1784 Dihedral : 6.683 111.585 1408 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.18 % Allowed : 22.84 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1268 helix: 2.05 (0.18), residues: 800 sheet: -1.27 (0.50), residues: 100 loop : -1.22 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.017 0.001 TYR B 66 PHE 0.026 0.001 PHE B 44 TRP 0.008 0.001 TRP Y 299 HIS 0.002 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00271 (10382) covalent geometry : angle 0.55540 (14024) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.05389 ( 2) hydrogen bonds : bond 0.04784 ( 636) hydrogen bonds : angle 4.30453 ( 1884) Misc. bond : bond 0.00146 ( 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 192 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.7868 (mmtm) cc_final: 0.7255 (mttt) REVERT: A 193 LYS cc_start: 0.8656 (tttt) cc_final: 0.8309 (ttpt) REVERT: A 207 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7900 (t0) REVERT: A 266 MET cc_start: 0.8403 (mtt) cc_final: 0.8165 (mtm) REVERT: A 297 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8351 (m-70) REVERT: A 370 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8220 (ptp) REVERT: A 447 LYS cc_start: 0.8215 (pttp) cc_final: 0.7880 (pttt) REVERT: A 457 GLN cc_start: 0.8565 (mt0) cc_final: 0.8322 (mm110) REVERT: A 473 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 557 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5130 (mmm) REVERT: A 576 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7758 (mmt90) REVERT: A 600 ASP cc_start: 0.6810 (OUTLIER) cc_final: 0.6554 (t70) REVERT: A 604 ARG cc_start: 0.8416 (ttp80) cc_final: 0.7961 (tmm-80) REVERT: A 608 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7919 (mt-10) REVERT: Y 9 MET cc_start: 0.2776 (OUTLIER) cc_final: 0.2247 (ptt) REVERT: Y 15 ARG cc_start: 0.6635 (ttp-110) cc_final: 0.6007 (ttm110) REVERT: Y 74 VAL cc_start: 0.8582 (OUTLIER) cc_final: 0.8362 (t) REVERT: Y 98 TRP cc_start: 0.5692 (m-10) cc_final: 0.5424 (m-10) REVERT: Y 130 TYR cc_start: 0.7596 (t80) cc_final: 0.7257 (t80) REVERT: Y 168 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6990 (tm-30) REVERT: Y 302 ARG cc_start: 0.6760 (ttp-110) cc_final: 0.6480 (ptm160) REVERT: Y 312 MET cc_start: 0.7758 (ttp) cc_final: 0.7474 (ttm) REVERT: E 17 LYS cc_start: 0.8244 (mttm) cc_final: 0.8009 (mmtt) outliers start: 35 outliers final: 23 residues processed: 182 average time/residue: 0.1191 time to fit residues: 30.0073 Evaluate side-chains 183 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 207 ASP 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 600 ASP 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 74 VAL Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 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 17 LEU 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 59 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 65 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.156754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120244 restraints weight = 11825.823| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.65 r_work: 0.3078 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10386 Z= 0.121 Angle : 0.552 7.846 14026 Z= 0.285 Chirality : 0.040 0.133 1615 Planarity : 0.004 0.053 1784 Dihedral : 6.577 110.456 1408 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.91 % Allowed : 23.11 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.24), residues: 1268 helix: 2.16 (0.18), residues: 800 sheet: -1.22 (0.50), residues: 100 loop : -1.20 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 327 TYR 0.018 0.001 TYR B 66 PHE 0.022 0.001 PHE B 44 TRP 0.008 0.001 TRP Y 299 HIS 0.006 0.001 HIS A 739 Details of bonding type rmsd covalent geometry : bond 0.00249 (10382) covalent geometry : angle 0.55189 (14024) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.06277 ( 2) hydrogen bonds : bond 0.04633 ( 636) hydrogen bonds : angle 4.24382 ( 1884) Misc. bond : bond 0.00134 ( 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 190 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.358 Fit side-chains REVERT: A 47 GLU cc_start: 0.7361 (tt0) cc_final: 0.6781 (mt-10) REVERT: A 54 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7196 (mttt) REVERT: A 193 LYS cc_start: 0.8637 (tttt) cc_final: 0.8265 (ttpt) REVERT: A 207 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7902 (t0) REVERT: A 297 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8354 (m-70) REVERT: A 370 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8248 (ptp) REVERT: A 447 LYS cc_start: 0.8121 (pttp) cc_final: 0.7784 (pttt) REVERT: A 457 GLN cc_start: 0.8572 (mt0) cc_final: 0.8342 (mm110) REVERT: A 473 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 485 ASN cc_start: 0.8324 (m110) cc_final: 0.7816 (m110) REVERT: A 534 ILE cc_start: 0.8767 (mt) cc_final: 0.8332 (tt) REVERT: A 557 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5167 (mmm) REVERT: A 576 ARG cc_start: 0.8033 (tpp80) cc_final: 0.7742 (mmt90) REVERT: A 583 LYS cc_start: 0.7993 (mttt) cc_final: 0.7326 (mmtp) REVERT: A 600 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.6515 (t70) REVERT: A 604 ARG cc_start: 0.8393 (ttp80) cc_final: 0.7908 (tmm-80) REVERT: A 608 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7907 (mt-10) REVERT: Y 9 MET cc_start: 0.2767 (OUTLIER) cc_final: 0.2248 (ptt) REVERT: Y 15 ARG cc_start: 0.6459 (ttp-110) cc_final: 0.5675 (ttm110) REVERT: Y 74 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8317 (t) REVERT: Y 98 TRP cc_start: 0.5699 (m-10) cc_final: 0.5333 (m-10) REVERT: Y 130 TYR cc_start: 0.7624 (t80) cc_final: 0.7327 (t80) REVERT: Y 168 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6915 (tm-30) REVERT: Y 302 ARG cc_start: 0.6734 (ttp-110) cc_final: 0.6446 (ptm160) REVERT: Y 312 MET cc_start: 0.7673 (ttp) cc_final: 0.7401 (ttm) REVERT: E 17 LYS cc_start: 0.8166 (mttm) cc_final: 0.7930 (mmtt) REVERT: B 43 MET cc_start: 0.5277 (ptt) cc_final: 0.3742 (mmm) outliers start: 32 outliers final: 23 residues processed: 182 average time/residue: 0.1200 time to fit residues: 30.0825 Evaluate side-chains 180 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 207 ASP 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 600 ASP Chi-restraints excluded: chain A residue 610 ILE 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 74 VAL Chi-restraints excluded: chain Y residue 118 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 143 ASN 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 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 10 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN Y 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.166572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136222 restraints weight = 11779.187| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.56 r_work: 0.3091 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3219 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= 0.134 Angle : 0.570 7.988 14026 Z= 0.293 Chirality : 0.041 0.176 1615 Planarity : 0.004 0.063 1784 Dihedral : 6.599 111.697 1408 Min Nonbonded Distance : 1.279 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.73 % Allowed : 23.38 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.24), residues: 1268 helix: 2.17 (0.18), residues: 799 sheet: -1.21 (0.50), residues: 100 loop : -1.21 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 10 TYR 0.018 0.001 TYR B 66 PHE 0.023 0.001 PHE Y 112 TRP 0.008 0.001 TRP Y 299 HIS 0.002 0.000 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00293 (10382) covalent geometry : angle 0.57008 (14024) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.08360 ( 2) hydrogen bonds : bond 0.04741 ( 636) hydrogen bonds : angle 4.23334 ( 1884) Misc. bond : bond 0.00154 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2982.90 seconds wall clock time: 51 minutes 42.54 seconds (3102.54 seconds total)