Starting phenix.real_space_refine on Sat Jun 7 15:34:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wix_32539/06_2025/7wix_32539.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wix_32539/06_2025/7wix_32539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wix_32539/06_2025/7wix_32539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wix_32539/06_2025/7wix_32539.map" model { file = "/net/cci-nas-00/data/ceres_data/7wix_32539/06_2025/7wix_32539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wix_32539/06_2025/7wix_32539.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 14 5.16 5 C 5521 2.51 5 N 1557 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4344 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 25, 'TRANS': 545} Chain: "B" Number of atoms: 4271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4271 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 25, 'TRANS': 550} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.81, per 1000 atoms: 0.67 Number of scatterers: 8670 At special positions: 0 Unit cell: (69.7, 98.4, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 4 15.00 Mg 1 11.99 O 1573 8.00 N 1557 7.00 C 5521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 66.8% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 322 Proline residue: A 310 - end of helix Processing helix chain 'A' and resid 326 through 375 removed outlier: 3.653A pdb=" N LEU A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 386 removed outlier: 4.055A pdb=" N PHE A 382 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 430 removed outlier: 4.875A pdb=" N VAL A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Proline residue: A 410 - end of helix Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 432 through 454 removed outlier: 4.268A pdb=" N GLY A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 455 through 479 removed outlier: 3.986A pdb=" N VAL A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 490 through 509 Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'A' and resid 523 through 541 removed outlier: 3.637A pdb=" N PHE A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 548 Processing helix chain 'A' and resid 549 through 556 Processing helix chain 'A' and resid 558 through 573 removed outlier: 3.636A pdb=" N LEU A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 564 " --> pdb=" O GLY A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'A' and resid 649 through 657 removed outlier: 4.588A pdb=" N ALA A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 677 Processing helix chain 'A' and resid 678 through 684 removed outlier: 3.705A pdb=" N TYR A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.705A pdb=" N PHE A 775 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 776 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP A 777 " --> pdb=" O ALA A 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 772 through 777' Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'B' and resid 13 through 45 removed outlier: 3.869A pdb=" N LEU B 17 " --> pdb=" O HIS B 13 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 49 through 52 removed outlier: 3.810A pdb=" N ARG B 52 " --> pdb=" O ALA B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 53 through 96 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 120 through 150 removed outlier: 3.575A pdb=" N LEU B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Proline residue: B 134 - end of helix Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 153 through 193 removed outlier: 4.264A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 202 through 209 Processing helix chain 'B' and resid 211 through 227 removed outlier: 4.028A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 238 through 265 removed outlier: 4.087A pdb=" N LEU B 242 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 292 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 293 through 312 removed outlier: 3.707A pdb=" N ILE B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 removed outlier: 4.056A pdb=" N LEU B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 406 removed outlier: 3.710A pdb=" N GLN B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 428 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 472 through 486 removed outlier: 3.678A pdb=" N VAL B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 514 removed outlier: 4.342A pdb=" N GLU B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.991A pdb=" N THR B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 572 removed outlier: 3.618A pdb=" N ALA B 572 " --> pdb=" O GLN B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 610 through 611 removed outlier: 3.629A pdb=" N ARG A 668 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 616 through 617 Processing sheet with id=AA3, first strand: chain 'A' and resid 768 through 770 removed outlier: 7.372A pdb=" N LEU A 769 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 639 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 355 removed outlier: 5.709A pdb=" N VAL B 337 " --> pdb=" O GLY B 351 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N SER B 353 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 335 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS B 355 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 333 " --> pdb=" O CYS B 355 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU B 333 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP B 335 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG B 389 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 490 through 494 removed outlier: 3.536A pdb=" N ILE B 523 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 363 " --> pdb=" O LEU B 538 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1407 1.31 - 1.43: 2266 1.43 - 1.56: 5134 1.56 - 1.68: 6 1.68 - 1.81: 23 Bond restraints: 8836 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C VAL A 611 " pdb=" O VAL A 611 " ideal model delta sigma weight residual 1.236 1.186 0.050 9.90e-03 1.02e+04 2.59e+01 bond pdb=" C5 ADP A 901 " pdb=" C6 ADP A 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C5 ADP B 601 " pdb=" C6 ADP B 601 " ideal model delta sigma weight residual 1.490 1.409 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 11738 2.42 - 4.85: 293 4.85 - 7.27: 36 7.27 - 9.70: 9 9.70 - 12.12: 5 Bond angle restraints: 12081 Sorted by residual: angle pdb=" N PRO A 607 " pdb=" CA PRO A 607 " pdb=" C PRO A 607 " ideal model delta sigma weight residual 112.47 101.44 11.03 2.06e+00 2.36e-01 2.87e+01 angle pdb=" O ALA B 229 " pdb=" C ALA B 229 " pdb=" N THR B 230 " ideal model delta sigma weight residual 121.47 125.36 -3.89 7.50e-01 1.78e+00 2.69e+01 angle pdb=" C ALA B 229 " pdb=" CA ALA B 229 " pdb=" CB ALA B 229 " ideal model delta sigma weight residual 117.07 110.29 6.78 1.44e+00 4.82e-01 2.22e+01 angle pdb=" CA ALA B 229 " pdb=" C ALA B 229 " pdb=" N THR B 230 " ideal model delta sigma weight residual 120.47 115.63 4.84 1.03e+00 9.43e-01 2.21e+01 angle pdb=" N THR A 522 " pdb=" CA THR A 522 " pdb=" C THR A 522 " ideal model delta sigma weight residual 114.75 108.95 5.80 1.26e+00 6.30e-01 2.12e+01 ... (remaining 12076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.86: 5033 28.86 - 57.73: 166 57.73 - 86.59: 20 86.59 - 115.46: 1 115.46 - 144.32: 3 Dihedral angle restraints: 5223 sinusoidal: 1962 harmonic: 3261 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 84.32 -144.32 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 69.06 -129.06 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 66.48 -126.48 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 5220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1306 0.068 - 0.136: 148 0.136 - 0.203: 12 0.203 - 0.271: 2 0.271 - 0.339: 2 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CA HIS B 227 " pdb=" N HIS B 227 " pdb=" C HIS B 227 " pdb=" CB HIS B 227 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CA THR B 230 " pdb=" N THR B 230 " pdb=" C THR B 230 " pdb=" CB THR B 230 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB THR B 230 " pdb=" CA THR B 230 " pdb=" OG1 THR B 230 " pdb=" CG2 THR B 230 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1467 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 97 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO B 98 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 605 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLU A 605 " -0.064 2.00e-02 2.50e+03 pdb=" O GLU A 605 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 606 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 836 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ARG A 836 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG A 836 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR A 837 " -0.018 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 106 2.63 - 3.20: 8317 3.20 - 3.77: 13404 3.77 - 4.33: 16835 4.33 - 4.90: 28731 Nonbonded interactions: 67393 Sorted by model distance: nonbonded pdb=" O1B ADP B 601 " pdb="MG MG B 602 " model vdw 2.063 2.170 nonbonded pdb=" OE2 GLU A 681 " pdb=" NH2 ARG A 685 " model vdw 2.237 3.120 nonbonded pdb=" O GLU A 605 " pdb=" CG2 THR A 609 " model vdw 2.261 3.460 nonbonded pdb=" O GLU B 465 " pdb=" OG SER B 468 " model vdw 2.264 3.040 nonbonded pdb=" O ASP A 680 " pdb=" OG1 THR A 684 " model vdw 2.279 3.040 ... (remaining 67388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.040 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.870 Find NCS groups from input model: 0.130 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 : 0.005 0.109 8836 Z= 0.266 Angle : 0.925 12.123 12081 Z= 0.550 Chirality : 0.045 0.339 1470 Planarity : 0.005 0.100 1538 Dihedral : 14.856 144.323 3121 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.15 % Favored : 89.50 % Rotamer: Outliers : 0.57 % Allowed : 6.70 % Favored : 92.73 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.22), residues: 1143 helix: -0.61 (0.18), residues: 711 sheet: -2.68 (0.61), residues: 62 loop : -4.20 (0.25), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 56 HIS 0.010 0.001 HIS B 227 PHE 0.024 0.001 PHE B 334 TYR 0.008 0.001 TYR A 736 ARG 0.003 0.000 ARG A 753 Details of bonding type rmsd hydrogen bonds : bond 0.12779 ( 522) hydrogen bonds : angle 5.55414 ( 1545) covalent geometry : bond 0.00466 ( 8836) covalent geometry : angle 0.92523 (12081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.880 Fit side-chains REVERT: A 691 GLN cc_start: 0.7183 (mm-40) cc_final: 0.6798 (mm-40) outliers start: 5 outliers final: 5 residues processed: 103 average time/residue: 0.2547 time to fit residues: 34.9897 Evaluate side-chains 62 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 232 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN A 582 HIS A 752 GLN B 204 GLN B 383 HIS B 420 HIS B 438 GLN B 504 ASN B 569 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064027 restraints weight = 23750.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.066017 restraints weight = 13029.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067388 restraints weight = 8796.276| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8836 Z= 0.253 Angle : 0.776 8.708 12081 Z= 0.387 Chirality : 0.045 0.164 1470 Planarity : 0.006 0.101 1538 Dihedral : 9.519 154.764 1279 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.27 % Favored : 90.55 % Rotamer: Outliers : 3.41 % Allowed : 13.64 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1143 helix: 0.51 (0.20), residues: 724 sheet: -1.88 (0.69), residues: 59 loop : -3.81 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 56 HIS 0.005 0.001 HIS A 827 PHE 0.035 0.002 PHE B 334 TYR 0.011 0.002 TYR A 444 ARG 0.003 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.05499 ( 522) hydrogen bonds : angle 4.90993 ( 1545) covalent geometry : bond 0.00579 ( 8836) covalent geometry : angle 0.77643 (12081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 750 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6928 (mt-10) outliers start: 30 outliers final: 16 residues processed: 88 average time/residue: 0.1806 time to fit residues: 23.7174 Evaluate side-chains 77 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.078626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.066816 restraints weight = 23649.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.068884 restraints weight = 12830.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.070323 restraints weight = 8585.790| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8836 Z= 0.137 Angle : 0.683 8.503 12081 Z= 0.335 Chirality : 0.042 0.165 1470 Planarity : 0.005 0.096 1538 Dihedral : 9.077 159.785 1278 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.75 % Favored : 91.08 % Rotamer: Outliers : 4.32 % Allowed : 16.25 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1143 helix: 1.18 (0.20), residues: 716 sheet: -1.69 (0.66), residues: 64 loop : -3.38 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.003 0.001 HIS A 827 PHE 0.023 0.001 PHE B 334 TYR 0.008 0.001 TYR A 837 ARG 0.004 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 522) hydrogen bonds : angle 4.45165 ( 1545) covalent geometry : bond 0.00292 ( 8836) covalent geometry : angle 0.68254 (12081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.948 Fit side-chains REVERT: A 750 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6823 (mt-10) outliers start: 38 outliers final: 25 residues processed: 95 average time/residue: 0.1948 time to fit residues: 26.8021 Evaluate side-chains 86 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3263 r_free = 0.3263 target = 0.079445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067643 restraints weight = 23446.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.069728 restraints weight = 12726.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.071156 restraints weight = 8516.105| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8836 Z= 0.128 Angle : 0.667 7.904 12081 Z= 0.324 Chirality : 0.041 0.161 1470 Planarity : 0.005 0.091 1538 Dihedral : 8.764 165.820 1275 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.75 % Favored : 91.08 % Rotamer: Outliers : 4.43 % Allowed : 17.39 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1143 helix: 1.42 (0.20), residues: 717 sheet: -1.33 (0.66), residues: 69 loop : -3.14 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.005 0.001 HIS A 582 PHE 0.016 0.001 PHE B 334 TYR 0.012 0.001 TYR A 444 ARG 0.006 0.000 ARG B 560 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 522) hydrogen bonds : angle 4.24324 ( 1545) covalent geometry : bond 0.00270 ( 8836) covalent geometry : angle 0.66717 (12081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8830 (tmmt) REVERT: A 750 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6818 (mt-10) outliers start: 39 outliers final: 27 residues processed: 97 average time/residue: 0.1749 time to fit residues: 25.3114 Evaluate side-chains 89 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 0.0020 chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.068184 restraints weight = 23532.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.070276 restraints weight = 12723.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071722 restraints weight = 8480.322| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8836 Z= 0.125 Angle : 0.660 11.577 12081 Z= 0.319 Chirality : 0.041 0.160 1470 Planarity : 0.005 0.090 1538 Dihedral : 8.720 173.838 1275 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.10 % Favored : 90.81 % Rotamer: Outliers : 3.98 % Allowed : 18.30 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1143 helix: 1.57 (0.20), residues: 717 sheet: -1.42 (0.63), residues: 74 loop : -2.94 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.003 0.001 HIS A 402 PHE 0.016 0.001 PHE B 334 TYR 0.008 0.001 TYR A 837 ARG 0.005 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 522) hydrogen bonds : angle 4.13620 ( 1545) covalent geometry : bond 0.00264 ( 8836) covalent geometry : angle 0.66009 (12081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.929 Fit side-chains REVERT: A 392 LYS cc_start: 0.9189 (tmtt) cc_final: 0.8958 (tmmt) REVERT: A 750 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6818 (mt-10) REVERT: B 231 MET cc_start: 0.7468 (mmm) cc_final: 0.7159 (mpp) REVERT: B 236 MET cc_start: 0.7575 (tmm) cc_final: 0.7185 (mmt) outliers start: 35 outliers final: 26 residues processed: 94 average time/residue: 0.1700 time to fit residues: 23.7817 Evaluate side-chains 89 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 0.0670 chunk 96 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.080561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.068857 restraints weight = 23309.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070965 restraints weight = 12637.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072409 restraints weight = 8427.659| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8836 Z= 0.122 Angle : 0.659 10.838 12081 Z= 0.317 Chirality : 0.041 0.162 1470 Planarity : 0.005 0.088 1538 Dihedral : 8.466 171.768 1274 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 4.55 % Allowed : 18.18 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1143 helix: 1.67 (0.20), residues: 716 sheet: -1.34 (0.63), residues: 74 loop : -2.84 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.004 0.001 HIS A 402 PHE 0.014 0.001 PHE B 334 TYR 0.016 0.001 TYR A 403 ARG 0.006 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 522) hydrogen bonds : angle 4.04328 ( 1545) covalent geometry : bond 0.00258 ( 8836) covalent geometry : angle 0.65885 (12081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 0.878 Fit side-chains REVERT: A 392 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8917 (tmmt) REVERT: A 454 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 750 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6816 (mt-10) REVERT: B 231 MET cc_start: 0.7339 (mmm) cc_final: 0.7115 (mpp) REVERT: B 236 MET cc_start: 0.7582 (tmm) cc_final: 0.7053 (mmt) outliers start: 40 outliers final: 32 residues processed: 93 average time/residue: 0.1799 time to fit residues: 24.6181 Evaluate side-chains 91 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 426 ASN ** 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 = 0.3243 r_free = 0.3243 target = 0.078398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066686 restraints weight = 23916.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068784 restraints weight = 12900.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.070198 restraints weight = 8597.523| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8836 Z= 0.170 Angle : 0.689 8.876 12081 Z= 0.334 Chirality : 0.042 0.162 1470 Planarity : 0.005 0.091 1538 Dihedral : 8.178 154.830 1274 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.10 % Favored : 90.81 % Rotamer: Outliers : 3.86 % Allowed : 20.45 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1143 helix: 1.67 (0.20), residues: 716 sheet: -1.21 (0.65), residues: 69 loop : -2.83 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.004 0.001 HIS A 402 PHE 0.022 0.001 PHE B 334 TYR 0.009 0.001 TYR A 444 ARG 0.009 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 522) hydrogen bonds : angle 4.18774 ( 1545) covalent geometry : bond 0.00382 ( 8836) covalent geometry : angle 0.68874 (12081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 236 MET cc_start: 0.7636 (tmm) cc_final: 0.7069 (mmt) REVERT: B 246 ILE cc_start: 0.9056 (mt) cc_final: 0.8744 (mt) REVERT: B 249 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7557 (mt0) outliers start: 34 outliers final: 28 residues processed: 87 average time/residue: 0.1822 time to fit residues: 23.8428 Evaluate side-chains 88 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.078769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.067017 restraints weight = 23923.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069105 restraints weight = 12791.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.070539 restraints weight = 8548.600| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8836 Z= 0.150 Angle : 0.696 10.504 12081 Z= 0.336 Chirality : 0.042 0.161 1470 Planarity : 0.005 0.091 1538 Dihedral : 7.730 137.413 1270 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.01 % Favored : 90.90 % Rotamer: Outliers : 4.09 % Allowed : 20.45 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.27), residues: 1143 helix: 1.71 (0.20), residues: 717 sheet: -1.20 (0.65), residues: 69 loop : -2.76 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 841 HIS 0.004 0.001 HIS A 402 PHE 0.019 0.001 PHE B 334 TYR 0.019 0.001 TYR A 403 ARG 0.006 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 522) hydrogen bonds : angle 4.13891 ( 1545) covalent geometry : bond 0.00333 ( 8836) covalent geometry : angle 0.69574 (12081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 236 MET cc_start: 0.7638 (tmm) cc_final: 0.7042 (mmt) REVERT: B 249 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7553 (mt0) outliers start: 36 outliers final: 31 residues processed: 86 average time/residue: 0.1806 time to fit residues: 23.3054 Evaluate side-chains 93 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.079206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.067476 restraints weight = 23710.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.069594 restraints weight = 12768.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.071041 restraints weight = 8510.887| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8836 Z= 0.139 Angle : 0.687 9.079 12081 Z= 0.331 Chirality : 0.042 0.173 1470 Planarity : 0.005 0.090 1538 Dihedral : 7.412 135.471 1270 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.75 % Favored : 91.16 % Rotamer: Outliers : 3.86 % Allowed : 20.45 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.27), residues: 1143 helix: 1.71 (0.20), residues: 718 sheet: -1.11 (0.65), residues: 69 loop : -2.71 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 841 HIS 0.005 0.001 HIS A 402 PHE 0.018 0.001 PHE B 334 TYR 0.008 0.001 TYR A 425 ARG 0.006 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 522) hydrogen bonds : angle 4.08730 ( 1545) covalent geometry : bond 0.00304 ( 8836) covalent geometry : angle 0.68743 (12081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 236 MET cc_start: 0.7635 (tmm) cc_final: 0.7050 (mmt) outliers start: 34 outliers final: 30 residues processed: 87 average time/residue: 0.2011 time to fit residues: 26.6080 Evaluate side-chains 92 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 77 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 61 optimal weight: 0.0980 chunk 40 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.081600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070009 restraints weight = 23579.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072176 restraints weight = 12607.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.073623 restraints weight = 8339.730| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8836 Z= 0.123 Angle : 0.683 10.802 12081 Z= 0.324 Chirality : 0.041 0.178 1470 Planarity : 0.005 0.088 1538 Dihedral : 6.985 132.359 1270 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 3.41 % Allowed : 21.14 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.27), residues: 1143 helix: 1.75 (0.20), residues: 720 sheet: -1.06 (0.64), residues: 69 loop : -2.67 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 841 HIS 0.004 0.000 HIS A 402 PHE 0.013 0.001 PHE B 334 TYR 0.017 0.001 TYR A 403 ARG 0.006 0.000 ARG A 751 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 522) hydrogen bonds : angle 3.93811 ( 1545) covalent geometry : bond 0.00246 ( 8836) covalent geometry : angle 0.68263 (12081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 236 MET cc_start: 0.7589 (tmm) cc_final: 0.6968 (mmt) outliers start: 30 outliers final: 30 residues processed: 86 average time/residue: 0.1763 time to fit residues: 22.7241 Evaluate side-chains 94 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 438 PHE Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 569 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3289 r_free = 0.3289 target = 0.080848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.069059 restraints weight = 23760.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.071209 restraints weight = 12774.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072696 restraints weight = 8491.343| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8836 Z= 0.129 Angle : 0.691 11.500 12081 Z= 0.329 Chirality : 0.042 0.200 1470 Planarity : 0.005 0.088 1538 Dihedral : 6.844 132.983 1270 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.05 % Favored : 91.86 % Rotamer: Outliers : 3.41 % Allowed : 21.48 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.27), residues: 1143 helix: 1.79 (0.20), residues: 719 sheet: -0.99 (0.65), residues: 69 loop : -2.61 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 841 HIS 0.005 0.001 HIS A 402 PHE 0.015 0.001 PHE B 334 TYR 0.007 0.001 TYR A 837 ARG 0.007 0.000 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 522) hydrogen bonds : angle 3.95674 ( 1545) covalent geometry : bond 0.00278 ( 8836) covalent geometry : angle 0.69071 (12081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.20 seconds wall clock time: 46 minutes 50.96 seconds (2810.96 seconds total)