Starting phenix.real_space_refine on Thu Feb 13 08:25:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wix_32539/02_2025/7wix_32539.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wix_32539/02_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_32539/02_2025/7wix_32539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wix_32539/02_2025/7wix_32539.map" model { file = "/net/cci-nas-00/data/ceres_data/7wix_32539/02_2025/7wix_32539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wix_32539/02_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-5592/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: 6.11, per 1000 atoms: 0.70 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: 2.35 Conformation dependent library (CDL) restraints added in 1.0 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: 0.87 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: 2.44 Time building geometry restraints manager: 2.72 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- 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= 0.330 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 *********************** 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 : 1.004 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: 0.2711 time to fit residues: 37.1251 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 : 0.907 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064019 restraints weight = 23750.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.066016 restraints weight = 13037.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067387 restraints weight = 8798.634| |-----------------------------------------------------------------------------| 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= 0.384 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 : 8.54 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 *********************** 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 : 0.954 Fit side-chains revert: symmetry clash REVERT: A 750 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6928 (mt-10) outliers start: 30 outliers final: 16 residues processed: 88 average time/residue: 0.1735 time to fit residues: 22.7563 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 : 0.895 ------------------------------------------------------------------------------- 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: 0.7980 chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.078491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.066704 restraints weight = 23654.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.068778 restraints weight = 12807.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.070217 restraints weight = 8554.566| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8836 Z= 0.195 Angle : 0.686 8.461 12081 Z= 0.337 Chirality : 0.042 0.165 1470 Planarity : 0.005 0.096 1538 Dihedral : 9.109 159.099 1278 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.66 % Favored : 91.16 % Rotamer: Outliers : 3.98 % Allowed : 16.36 % Favored : 79.66 % 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: -0.57 (0.26), residues: 1143 helix: 1.17 (0.20), residues: 714 sheet: -1.71 (0.66), residues: 64 loop : -3.42 (0.29), residues: 365 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 0.024 0.001 PHE B 334 TYR 0.008 0.001 TYR A 837 ARG 0.004 0.000 ARG A 385 *********************** 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 101 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 66 time to evaluate : 0.976 Fit side-chains REVERT: A 750 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6813 (mt-10) outliers start: 35 outliers final: 25 residues processed: 91 average time/residue: 0.1764 time to fit residues: 24.0241 Evaluate side-chains 85 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.078873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.067108 restraints weight = 23483.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069189 restraints weight = 12715.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.070537 restraints weight = 8499.128| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8836 Z= 0.192 Angle : 0.668 7.954 12081 Z= 0.327 Chirality : 0.041 0.161 1470 Planarity : 0.005 0.092 1538 Dihedral : 8.803 164.935 1275 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.84 % Favored : 90.99 % Rotamer: Outliers : 4.32 % Allowed : 17.84 % Favored : 77.84 % 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: -0.18 (0.26), residues: 1143 helix: 1.40 (0.20), residues: 717 sheet: -1.36 (0.66), residues: 69 loop : -3.17 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 841 HIS 0.005 0.001 HIS A 582 PHE 0.018 0.001 PHE B 334 TYR 0.012 0.001 TYR A 444 ARG 0.004 0.000 ARG A 385 *********************** 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 108 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 0.889 Fit side-chains REVERT: A 392 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8830 (tmmt) REVERT: A 750 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6818 (mt-10) REVERT: B 231 MET cc_start: 0.7507 (mmm) cc_final: 0.6948 (mmm) outliers start: 38 outliers final: 26 residues processed: 100 average time/residue: 0.1931 time to fit residues: 27.5848 Evaluate side-chains 87 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 587 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 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 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: 0.7980 chunk 109 optimal weight: 0.0000 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 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 703 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.080209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.068402 restraints weight = 23448.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070500 restraints weight = 12724.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.071935 restraints weight = 8509.546| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.169 Angle : 0.658 10.688 12081 Z= 0.318 Chirality : 0.041 0.160 1470 Planarity : 0.005 0.091 1538 Dihedral : 8.717 172.967 1275 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 3.98 % Allowed : 18.41 % Favored : 77.61 % 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: 1.56 (0.20), residues: 717 sheet: -1.43 (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 0.014 0.001 PHE B 334 TYR 0.008 0.001 TYR A 837 ARG 0.008 0.000 ARG B 560 *********************** 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 104 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 0.948 Fit side-chains REVERT: A 392 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8924 (tmmt) REVERT: A 397 ASP cc_start: 0.7642 (m-30) cc_final: 0.7246 (m-30) REVERT: A 750 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6815 (mt-10) REVERT: B 231 MET cc_start: 0.7487 (mmm) cc_final: 0.7151 (mpp) outliers start: 35 outliers final: 26 residues processed: 96 average time/residue: 0.1770 time to fit residues: 25.5899 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 : 0.946 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 83 optimal weight: 0.0050 chunk 96 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.080421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.068694 restraints weight = 23295.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.070806 restraints weight = 12627.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.072247 restraints weight = 8432.325| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2168 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= 0.171 Angle : 0.663 10.071 12081 Z= 0.318 Chirality : 0.041 0.162 1470 Planarity : 0.005 0.089 1538 Dihedral : 8.613 176.583 1274 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.40 % Favored : 91.51 % Rotamer: Outliers : 3.75 % Allowed : 19.09 % Favored : 77.16 % 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: 0.22 (0.26), residues: 1143 helix: 1.65 (0.20), residues: 717 sheet: -1.32 (0.63), residues: 74 loop : -2.84 (0.31), residues: 352 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 0.015 0.001 PHE B 334 TYR 0.015 0.001 TYR A 403 ARG 0.005 0.000 ARG A 385 *********************** 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 98 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.901 Fit side-chains REVERT: A 454 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 750 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6819 (mt-10) REVERT: B 231 MET cc_start: 0.7407 (mmm) cc_final: 0.7174 (mpp) REVERT: B 236 MET cc_start: 0.7551 (tmm) cc_final: 0.7132 (mmt) REVERT: B 249 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7576 (mt0) outliers start: 33 outliers final: 26 residues processed: 90 average time/residue: 0.1760 time to fit residues: 23.5282 Evaluate side-chains 88 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 234 LEU Chi-restraints excluded: chain B residue 249 GLN 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 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: 1.9990 chunk 90 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.078603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066873 restraints weight = 23888.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.068961 restraints weight = 12889.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.070375 restraints weight = 8583.399| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8836 Z= 0.230 Angle : 0.687 9.401 12081 Z= 0.332 Chirality : 0.042 0.163 1470 Planarity : 0.005 0.091 1538 Dihedral : 8.127 158.267 1270 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.19 % Favored : 90.73 % Rotamer: Outliers : 4.66 % Allowed : 19.20 % Favored : 76.14 % 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 (0.26), residues: 1143 helix: 1.65 (0.20), residues: 717 sheet: -1.19 (0.65), residues: 69 loop : -2.82 (0.31), residues: 357 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 0.021 0.001 PHE B 334 TYR 0.009 0.001 TYR A 444 ARG 0.008 0.000 ARG A 751 *********************** 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 100 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 59 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 236 MET cc_start: 0.7635 (tmm) cc_final: 0.7106 (mmt) REVERT: B 246 ILE cc_start: 0.9032 (mt) cc_final: 0.8712 (mt) REVERT: B 249 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7567 (mt0) outliers start: 41 outliers final: 30 residues processed: 89 average time/residue: 0.1765 time to fit residues: 23.4194 Evaluate side-chains 89 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.4980 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.080107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.068376 restraints weight = 23822.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.070491 restraints weight = 12784.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.071875 restraints weight = 8505.339| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8836 Z= 0.176 Angle : 0.684 10.268 12081 Z= 0.328 Chirality : 0.042 0.161 1470 Planarity : 0.005 0.089 1538 Dihedral : 7.677 138.170 1270 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.66 % Favored : 91.25 % Rotamer: Outliers : 3.98 % Allowed : 19.77 % Favored : 76.25 % 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: 0.35 (0.27), residues: 1143 helix: 1.71 (0.20), residues: 717 sheet: -1.13 (0.65), residues: 69 loop : -2.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 841 HIS 0.004 0.001 HIS A 402 PHE 0.014 0.001 PHE B 334 TYR 0.019 0.001 TYR A 403 ARG 0.007 0.000 ARG A 751 *********************** 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 98 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 236 MET cc_start: 0.7621 (tmm) cc_final: 0.7047 (mmt) outliers start: 35 outliers final: 29 residues processed: 87 average time/residue: 0.1787 time to fit residues: 23.0236 Evaluate side-chains 90 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 103 optimal weight: 0.0170 chunk 102 optimal weight: 6.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.080246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.068547 restraints weight = 23659.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070677 restraints weight = 12688.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072132 restraints weight = 8425.202| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2415 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= 0.183 Angle : 0.685 10.191 12081 Z= 0.329 Chirality : 0.041 0.161 1470 Planarity : 0.005 0.088 1538 Dihedral : 7.298 133.492 1270 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.75 % Favored : 91.16 % Rotamer: Outliers : 3.30 % Allowed : 20.45 % Favored : 76.25 % 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: 0.39 (0.27), residues: 1143 helix: 1.72 (0.20), residues: 717 sheet: -1.06 (0.64), residues: 69 loop : -2.66 (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 0.015 0.001 PHE B 334 TYR 0.014 0.001 TYR A 444 ARG 0.006 0.000 ARG A 385 *********************** 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 92 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 236 MET cc_start: 0.7592 (tmm) cc_final: 0.7050 (mmt) outliers start: 29 outliers final: 29 residues processed: 83 average time/residue: 0.1829 time to fit residues: 22.5162 Evaluate side-chains 90 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 89 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 overall best weight: 0.4208 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.082198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.070581 restraints weight = 23547.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.072745 restraints weight = 12611.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.074222 restraints weight = 8352.849| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2624 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= 0.162 Angle : 0.675 10.553 12081 Z= 0.321 Chirality : 0.041 0.160 1470 Planarity : 0.005 0.087 1538 Dihedral : 6.804 130.742 1270 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.70 % Favored : 92.21 % Rotamer: Outliers : 3.41 % Allowed : 20.68 % Favored : 75.91 % 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: 0.50 (0.27), residues: 1143 helix: 1.79 (0.20), residues: 719 sheet: -1.02 (0.64), residues: 69 loop : -2.59 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 841 HIS 0.005 0.000 HIS A 402 PHE 0.012 0.001 PHE B 334 TYR 0.018 0.001 TYR A 403 ARG 0.006 0.000 ARG A 751 ********************** 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 99 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 454 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7769 (tm-30) REVERT: A 750 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6756 (mt-10) REVERT: B 236 MET cc_start: 0.7565 (tmm) cc_final: 0.6991 (mmt) outliers start: 30 outliers final: 29 residues processed: 91 average time/residue: 0.1709 time to fit residues: 23.5443 Evaluate side-chains 92 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 9 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 67 optimal weight: 0.0070 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.081141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069454 restraints weight = 23793.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.071595 restraints weight = 12800.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073051 restraints weight = 8503.521| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2633 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= 0.180 Angle : 0.688 10.508 12081 Z= 0.326 Chirality : 0.041 0.160 1470 Planarity : 0.005 0.087 1538 Dihedral : 6.700 131.622 1270 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 3.64 % Allowed : 20.68 % 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: 0.55 (0.26), residues: 1143 helix: 1.81 (0.20), residues: 719 sheet: -0.93 (0.65), residues: 69 loop : -2.55 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 841 HIS 0.004 0.001 HIS A 402 PHE 0.014 0.001 PHE B 334 TYR 0.007 0.001 TYR A 568 ARG 0.005 0.000 ARG A 751 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.38 seconds wall clock time: 42 minutes 18.28 seconds (2538.28 seconds total)