Starting phenix.real_space_refine on Fri Sep 11 00:05:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eja_48098/09_2026/9eja_48098.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eja_48098/09_2026/9eja_48098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eja_48098/09_2026/9eja_48098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eja_48098/09_2026/9eja_48098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eja_48098/09_2026/9eja_48098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eja_48098/09_2026/9eja_48098.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 3532 2.51 5 N 977 2.21 5 O 1064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5626 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5403 Classifications: {'peptide': 676} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 655} Chain breaks: 3 Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'AGS': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1380 SG CYS A 350 21.083 52.663 39.028 1.00 58.23 S ATOM 1054 SG CYS A 310 16.527 52.597 36.218 1.00 83.50 S ATOM 967 SG CYS A 298 19.125 48.310 35.537 1.00 74.53 S ATOM 846 SG CYS A 283 17.387 48.846 40.912 1.00 87.63 S Time building chain proxies: 1.64, per 1000 atoms: 0.29 Number of scatterers: 5626 At special positions: 0 Unit cell: (67.896, 81.972, 101.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 36 16.00 P 12 15.00 Mg 1 11.99 O 1064 8.00 N 977 7.00 C 3532 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: 0.51 Conformation dependent library (CDL) restraints added in 371.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1303 " pdb="FE3 SF4 A1303 " - pdb=" SG CYS A 298 " pdb="FE2 SF4 A1303 " - pdb=" SG CYS A 310 " pdb="FE1 SF4 A1303 " - pdb=" SG CYS A 350 " pdb="FE4 SF4 A1303 " - pdb=" SG CYS A 283 " Number of angles added : 12 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1272 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 57.5% alpha, 6.7% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.554A pdb=" N VAL A 13 " --> pdb=" O ILE A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.857A pdb=" N MET A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.624A pdb=" N GLY A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.690A pdb=" N GLY A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.800A pdb=" N GLU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.525A pdb=" N GLY A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N HIS A 317 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 327 removed outlier: 3.938A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.501A pdb=" N THR A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.557A pdb=" N ASP A 374 " --> pdb=" O ASN A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.649A pdb=" N MET A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 406 Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.825A pdb=" N ASN A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.557A pdb=" N GLU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.730A pdb=" N GLN A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 543 removed outlier: 6.281A pdb=" N GLN A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 removed outlier: 4.564A pdb=" N ASP A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.715A pdb=" N THR A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 687 Processing helix chain 'A' and resid 697 through 712 Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 731 through 748 removed outlier: 4.033A pdb=" N PHE A 735 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 738 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.986A pdb=" N ALA A 776 " --> pdb=" O ASP A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 804 Processing helix chain 'A' and resid 812 through 830 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 861 through 866 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.513A pdb=" N HIS A 888 " --> pdb=" O PHE A 884 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 390 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 250 removed outlier: 6.097A pdb=" N THR A 274 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.636A pdb=" N VAL A 588 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 647 removed outlier: 3.810A pdb=" N TRP A 647 " --> pdb=" O GLY A 840 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 692 through 694 removed outlier: 5.878A pdb=" N LEU A 692 " --> pdb=" O ILE A 780 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 782 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 694 " --> pdb=" O ILE A 782 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 845 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 781 " --> pdb=" O VAL A 845 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 722 through 723 removed outlier: 5.714A pdb=" N THR A 722 " --> pdb=" O LEU A 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 244 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 2449 1.42 - 1.63: 3259 1.63 - 1.85: 44 1.85 - 2.06: 1 2.06 - 2.27: 12 Bond restraints: 5765 Sorted by residual: bond pdb=" C LEU A 276 " pdb=" N SER A 277 " ideal model delta sigma weight residual 1.329 1.458 -0.128 1.15e-02 7.56e+03 1.24e+02 bond pdb=" O3B AGS A1301 " pdb=" PB AGS A1301 " ideal model delta sigma weight residual 1.673 1.576 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O3A AGS A1301 " pdb=" PA AGS A1301 " ideal model delta sigma weight residual 1.664 1.578 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta sigma weight residual 1.452 1.497 -0.044 1.18e-02 7.18e+03 1.41e+01 bond pdb=" CA TYR A 353 " pdb=" C TYR A 353 " ideal model delta sigma weight residual 1.521 1.471 0.049 1.36e-02 5.41e+03 1.31e+01 ... (remaining 5760 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 7629 2.24 - 4.47: 153 4.47 - 6.71: 46 6.71 - 8.95: 8 8.95 - 11.18: 7 Bond angle restraints: 7843 Sorted by residual: angle pdb=" C LEU A 719 " pdb=" N VAL A 720 " pdb=" CA VAL A 720 " ideal model delta sigma weight residual 122.63 116.10 6.53 1.19e+00 7.06e-01 3.01e+01 angle pdb=" N ILE A 603 " pdb=" CA ILE A 603 " pdb=" C ILE A 603 " ideal model delta sigma weight residual 113.71 108.57 5.14 9.50e-01 1.11e+00 2.93e+01 angle pdb=" C LEU A 276 " pdb=" N SER A 277 " pdb=" CA SER A 277 " ideal model delta sigma weight residual 122.20 113.82 8.38 1.72e+00 3.38e-01 2.38e+01 angle pdb=" O HIS A 281 " pdb=" C HIS A 281 " pdb=" N THR A 282 " ideal model delta sigma weight residual 122.34 127.42 -5.08 1.10e+00 8.26e-01 2.13e+01 angle pdb=" CA HIS A 281 " pdb=" C HIS A 281 " pdb=" N THR A 282 " ideal model delta sigma weight residual 118.81 113.57 5.24 1.15e+00 7.56e-01 2.08e+01 ... (remaining 7838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 3125 29.78 - 59.55: 298 59.55 - 89.32: 23 89.32 - 119.10: 2 119.10 - 148.87: 3 Dihedral angle restraints: 3451 sinusoidal: 1481 harmonic: 1970 Sorted by residual: dihedral pdb=" CA LYS A 348 " pdb=" C LYS A 348 " pdb=" N ALA A 349 " pdb=" CA ALA A 349 " ideal model delta harmonic sigma weight residual -180.00 -151.17 -28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" O1B AGS A1301 " pdb=" O3B AGS A1301 " pdb=" PB AGS A1301 " pdb=" PG AGS A1301 " ideal model delta sinusoidal sigma weight residual 138.55 -10.32 148.87 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" O2B AGS A1301 " pdb=" O3B AGS A1301 " pdb=" PB AGS A1301 " pdb=" PG AGS A1301 " ideal model delta sinusoidal sigma weight residual 7.37 -134.37 141.74 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 3448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.138: 867 4.138 - 8.277: 0 8.277 - 12.415: 0 12.415 - 16.553: 0 16.553 - 20.692: 4 Chirality restraints: 871 Sorted by residual: chirality pdb="FE1 SF4 A1303 " pdb=" S2 SF4 A1303 " pdb=" S3 SF4 A1303 " pdb=" S4 SF4 A1303 " both_signs ideal model delta sigma weight residual False -10.55 10.14 -20.69 2.00e-01 2.50e+01 1.07e+04 chirality pdb="FE3 SF4 A1303 " pdb=" S1 SF4 A1303 " pdb=" S2 SF4 A1303 " pdb=" S4 SF4 A1303 " both_signs ideal model delta sigma weight residual False -10.55 10.13 -20.68 2.00e-01 2.50e+01 1.07e+04 chirality pdb="FE2 SF4 A1303 " pdb=" S1 SF4 A1303 " pdb=" S3 SF4 A1303 " pdb=" S4 SF4 A1303 " both_signs ideal model delta sigma weight residual False 10.55 -10.12 20.67 2.00e-01 2.50e+01 1.07e+04 ... (remaining 868 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 276 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LEU A 276 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 276 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 277 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 779 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C VAL A 779 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL A 779 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 780 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 39 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C LYS A 39 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS A 39 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 40 " 0.011 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 680 2.75 - 3.29: 5420 3.29 - 3.82: 9626 3.82 - 4.36: 11357 4.36 - 4.90: 19295 Nonbonded interactions: 46378 Sorted by model distance: nonbonded pdb=" OH TYR A 698 " pdb=" OE2 GLU A 726 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O ASP A 393 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 856 " pdb=" OP1 DA B 3 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 6 " pdb=" O PHE A 17 " model vdw 2.233 3.040 nonbonded pdb=" O HIS A 323 " pdb=" OG1 THR A 327 " model vdw 2.251 3.040 ... (remaining 46373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.490 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.016 0.872 5769 Z= 0.555 Angle : 0.953 26.635 7855 Z= 0.496 Chirality : 1.400 20.692 871 Planarity : 0.005 0.047 960 Dihedral : 21.188 148.874 2179 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.05 % Allowed : 31.48 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.32), residues: 668 helix: 0.26 (0.28), residues: 320 sheet: -1.20 (0.64), residues: 77 loop : -2.03 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 836 TYR 0.015 0.002 TYR A 742 PHE 0.024 0.002 PHE A 884 TRP 0.012 0.002 TRP A 5 HIS 0.007 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.34 ( 5765) covalent geometry : angle 0.86834 / 0.50 ( 7843) hydrogen bonds : bond 0.16865 / 10.75 ( 244) hydrogen bonds : angle 6.69472 / 4.55 ( 708) metal coordination : bond 0.56730 / 27.59 ( 4) metal coordination : angle 10.11276 / 5.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.5730 (t80) REVERT: A 341 VAL cc_start: 0.8093 (t) cc_final: 0.7796 (t) REVERT: A 528 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7018 (ttpt) REVERT: A 587 HIS cc_start: 0.6885 (m90) cc_final: 0.6339 (m170) REVERT: A 664 PHE cc_start: 0.6878 (t80) cc_final: 0.6443 (t80) REVERT: A 802 ASP cc_start: 0.8588 (m-30) cc_final: 0.8288 (m-30) REVERT: A 822 TYR cc_start: 0.8519 (m-80) cc_final: 0.7972 (m-80) REVERT: A 836 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7390 (tpp-160) outliers start: 30 outliers final: 22 residues processed: 114 average time/residue: 0.0703 time to fit residues: 10.8251 Evaluate side-chains 114 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.170398 restraints weight = 5730.697| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.25 r_work: 0.3929 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.265 5769 Z= 0.411 Angle : 2.474 50.749 7855 Z= 1.409 Chirality : 0.427 6.333 871 Planarity : 0.005 0.043 960 Dihedral : 15.740 123.219 914 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.89 % Allowed : 29.97 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.34), residues: 668 helix: 0.86 (0.29), residues: 326 sheet: -1.48 (0.62), residues: 77 loop : -2.04 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 865 TYR 0.010 0.001 TYR A 822 PHE 0.017 0.002 PHE A 884 TRP 0.010 0.001 TRP A 335 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01182 / 0.41 ( 5765) covalent geometry : angle 2.14010 / 1.41 ( 7843) hydrogen bonds : bond 0.04549 / 2.85 ( 244) hydrogen bonds : angle 4.99534 / 3.36 ( 708) metal coordination : bond 0.02743 / 1.38 ( 4) metal coordination : angle 31.82903 / 17.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 19 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5726 (t80) REVERT: A 341 VAL cc_start: 0.8179 (t) cc_final: 0.7853 (t) REVERT: A 360 GLN cc_start: 0.7749 (pp30) cc_final: 0.7452 (pp30) REVERT: A 587 HIS cc_start: 0.6882 (m90) cc_final: 0.6353 (m170) REVERT: A 604 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8141 (t0) REVERT: A 640 ILE cc_start: 0.7661 (mm) cc_final: 0.7406 (tp) REVERT: A 664 PHE cc_start: 0.6796 (t80) cc_final: 0.6301 (t80) REVERT: A 802 ASP cc_start: 0.8612 (m-30) cc_final: 0.8387 (m-30) REVERT: A 822 TYR cc_start: 0.8439 (m-80) cc_final: 0.8005 (m-80) REVERT: A 836 ARG cc_start: 0.7541 (tpp80) cc_final: 0.7280 (tpp-160) outliers start: 35 outliers final: 25 residues processed: 119 average time/residue: 0.0631 time to fit residues: 10.3390 Evaluate side-chains 112 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.203063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.167195 restraints weight = 5669.845| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.28 r_work: 0.3907 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 5769 Z= 0.399 Angle : 2.473 50.434 7855 Z= 1.406 Chirality : 0.429 6.316 871 Planarity : 0.005 0.045 960 Dihedral : 14.871 105.571 896 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.72 % Allowed : 29.80 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.34), residues: 668 helix: 1.09 (0.29), residues: 325 sheet: -1.52 (0.62), residues: 77 loop : -2.03 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 707 TYR 0.010 0.001 TYR A 822 PHE 0.020 0.002 PHE A 884 TRP 0.011 0.001 TRP A 335 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01151 / 0.40 ( 5765) covalent geometry : angle 2.13344 / 1.40 ( 7843) hydrogen bonds : bond 0.04075 / 2.51 ( 244) hydrogen bonds : angle 4.75695 / 3.18 ( 708) metal coordination : bond 0.02878 / 1.47 ( 4) metal coordination : angle 32.04546 / 17.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 19 TYR cc_start: 0.6507 (OUTLIER) cc_final: 0.5696 (t80) REVERT: A 341 VAL cc_start: 0.8192 (t) cc_final: 0.7855 (t) REVERT: A 360 GLN cc_start: 0.7771 (pp30) cc_final: 0.7459 (pp30) REVERT: A 587 HIS cc_start: 0.6936 (m90) cc_final: 0.6406 (m170) REVERT: A 604 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8141 (t0) REVERT: A 640 ILE cc_start: 0.7693 (mm) cc_final: 0.7419 (tp) REVERT: A 664 PHE cc_start: 0.6829 (t80) cc_final: 0.6277 (t80) REVERT: A 671 GLU cc_start: 0.6571 (mp0) cc_final: 0.6033 (mp0) REVERT: A 802 ASP cc_start: 0.8615 (m-30) cc_final: 0.8372 (m-30) REVERT: A 822 TYR cc_start: 0.8445 (m-80) cc_final: 0.8001 (m-80) REVERT: A 836 ARG cc_start: 0.7585 (tpp80) cc_final: 0.7356 (tpp-160) outliers start: 34 outliers final: 24 residues processed: 118 average time/residue: 0.0627 time to fit residues: 10.1266 Evaluate side-chains 118 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 HIS ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.200628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.166027 restraints weight = 5799.125| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.18 r_work: 0.3874 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 5769 Z= 0.417 Angle : 2.487 50.568 7855 Z= 1.410 Chirality : 0.429 6.353 871 Planarity : 0.005 0.049 960 Dihedral : 14.275 94.184 889 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.73 % Allowed : 28.79 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.34), residues: 668 helix: 1.09 (0.29), residues: 326 sheet: -1.71 (0.61), residues: 77 loop : -2.04 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 707 TYR 0.013 0.002 TYR A 822 PHE 0.020 0.002 PHE A 884 TRP 0.014 0.002 TRP A 335 HIS 0.007 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.01181 / 0.42 ( 5765) covalent geometry : angle 2.14197 / 1.41 ( 7843) hydrogen bonds : bond 0.03888 / 2.46 ( 244) hydrogen bonds : angle 4.77948 / 3.21 ( 708) metal coordination : bond 0.03178 / 1.62 ( 4) metal coordination : angle 32.38295 / 17.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6272 (m-80) cc_final: 0.5888 (t80) REVERT: A 19 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.5544 (t80) REVERT: A 29 MET cc_start: 0.6789 (mtt) cc_final: 0.6159 (mtt) REVERT: A 341 VAL cc_start: 0.8250 (t) cc_final: 0.7925 (t) REVERT: A 587 HIS cc_start: 0.6950 (m90) cc_final: 0.6427 (m170) REVERT: A 604 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8171 (t0) REVERT: A 625 SER cc_start: 0.7874 (OUTLIER) cc_final: 0.7581 (m) REVERT: A 640 ILE cc_start: 0.7708 (mm) cc_final: 0.7397 (tp) REVERT: A 641 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7043 (pp) REVERT: A 664 PHE cc_start: 0.6953 (t80) cc_final: 0.6392 (t80) REVERT: A 802 ASP cc_start: 0.8657 (m-30) cc_final: 0.8454 (m-30) REVERT: A 822 TYR cc_start: 0.8495 (m-80) cc_final: 0.7956 (m-80) REVERT: A 836 ARG cc_start: 0.7615 (tpp80) cc_final: 0.7319 (tpp-160) outliers start: 40 outliers final: 30 residues processed: 118 average time/residue: 0.0660 time to fit residues: 10.5789 Evaluate side-chains 122 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 873 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.201089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.166033 restraints weight = 5879.601| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.24 r_work: 0.3875 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 5769 Z= 0.406 Angle : 2.478 50.516 7855 Z= 1.407 Chirality : 0.429 6.333 871 Planarity : 0.005 0.047 960 Dihedral : 13.931 84.639 889 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 7.07 % Allowed : 28.45 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.34), residues: 668 helix: 1.15 (0.29), residues: 326 sheet: -1.78 (0.61), residues: 77 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.014 0.002 TYR A 247 PHE 0.018 0.002 PHE A 884 TRP 0.014 0.001 TRP A 335 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01163 / 0.41 ( 5765) covalent geometry : angle 2.13406 / 1.40 ( 7843) hydrogen bonds : bond 0.03688 / 2.32 ( 244) hydrogen bonds : angle 4.74696 / 3.19 ( 708) metal coordination : bond 0.02685 / 1.37 ( 4) metal coordination : angle 32.27012 / 17.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6196 (m-80) cc_final: 0.5843 (t80) REVERT: A 19 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.5751 (t80) REVERT: A 29 MET cc_start: 0.6805 (mtt) cc_final: 0.6189 (mtt) REVERT: A 341 VAL cc_start: 0.8272 (t) cc_final: 0.7944 (t) REVERT: A 528 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7138 (ttpt) REVERT: A 587 HIS cc_start: 0.7001 (m90) cc_final: 0.6465 (m170) REVERT: A 625 SER cc_start: 0.7875 (OUTLIER) cc_final: 0.7603 (m) REVERT: A 664 PHE cc_start: 0.6957 (t80) cc_final: 0.6384 (t80) REVERT: A 822 TYR cc_start: 0.8476 (m-80) cc_final: 0.7940 (m-80) REVERT: A 836 ARG cc_start: 0.7612 (tpp80) cc_final: 0.7361 (tpp-160) outliers start: 42 outliers final: 32 residues processed: 119 average time/residue: 0.0654 time to fit residues: 10.5410 Evaluate side-chains 123 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 761 CYS Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.202575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167905 restraints weight = 5753.120| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.24 r_work: 0.3896 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 5769 Z= 0.390 Angle : 2.475 50.489 7855 Z= 1.405 Chirality : 0.428 6.318 871 Planarity : 0.004 0.043 960 Dihedral : 13.573 81.842 888 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.57 % Allowed : 29.46 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.34), residues: 668 helix: 1.26 (0.29), residues: 326 sheet: -1.68 (0.61), residues: 77 loop : -2.02 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.011 0.001 TYR A 247 PHE 0.025 0.002 PHE A 884 TRP 0.012 0.001 TRP A 335 HIS 0.009 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.01135 / 0.39 ( 5765) covalent geometry : angle 2.12925 / 1.40 ( 7843) hydrogen bonds : bond 0.03502 / 2.21 ( 244) hydrogen bonds : angle 4.62466 / 3.12 ( 708) metal coordination : bond 0.02133 / 1.09 ( 4) metal coordination : angle 32.35250 / 17.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6161 (m-80) cc_final: 0.5820 (t80) REVERT: A 19 TYR cc_start: 0.6582 (OUTLIER) cc_final: 0.5764 (t80) REVERT: A 29 MET cc_start: 0.6720 (mtt) cc_final: 0.6146 (mtt) REVERT: A 341 VAL cc_start: 0.8243 (t) cc_final: 0.7910 (t) REVERT: A 528 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7105 (ttpt) REVERT: A 587 HIS cc_start: 0.6944 (m90) cc_final: 0.6418 (m170) REVERT: A 625 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7570 (m) REVERT: A 640 ILE cc_start: 0.7687 (mm) cc_final: 0.7355 (tp) REVERT: A 664 PHE cc_start: 0.6956 (t80) cc_final: 0.6375 (t80) REVERT: A 738 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6338 (pp) REVERT: A 822 TYR cc_start: 0.8441 (m-80) cc_final: 0.7971 (m-80) REVERT: A 836 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7435 (tpp-160) outliers start: 39 outliers final: 31 residues processed: 121 average time/residue: 0.0655 time to fit residues: 10.7285 Evaluate side-chains 125 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 HIS ** 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 = 0.4376 r_free = 0.4376 target = 0.203084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.168207 restraints weight = 5838.775| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.25 r_work: 0.3885 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 5769 Z= 0.388 Angle : 2.473 50.480 7855 Z= 1.404 Chirality : 0.428 6.312 871 Planarity : 0.004 0.042 960 Dihedral : 13.332 80.499 888 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.90 % Allowed : 29.46 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.34), residues: 668 helix: 1.32 (0.29), residues: 326 sheet: -1.68 (0.59), residues: 77 loop : -2.01 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.011 0.001 TYR A 743 PHE 0.020 0.002 PHE A 884 TRP 0.012 0.001 TRP A 335 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.39 ( 5765) covalent geometry : angle 2.12917 / 1.40 ( 7843) hydrogen bonds : bond 0.03477 / 2.19 ( 244) hydrogen bonds : angle 4.61188 / 3.12 ( 708) metal coordination : bond 0.01988 / 1.01 ( 4) metal coordination : angle 32.26472 / 17.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6167 (m-80) cc_final: 0.5844 (t80) REVERT: A 19 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.5762 (t80) REVERT: A 28 MET cc_start: 0.6804 (mtp) cc_final: 0.6603 (mtp) REVERT: A 29 MET cc_start: 0.6681 (mtt) cc_final: 0.6011 (mtt) REVERT: A 341 VAL cc_start: 0.8239 (t) cc_final: 0.7902 (t) REVERT: A 528 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7065 (ttpt) REVERT: A 587 HIS cc_start: 0.6957 (m90) cc_final: 0.6418 (m170) REVERT: A 625 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7525 (m) REVERT: A 640 ILE cc_start: 0.7652 (mm) cc_final: 0.7335 (tp) REVERT: A 664 PHE cc_start: 0.6977 (t80) cc_final: 0.6407 (t80) REVERT: A 738 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6319 (pp) REVERT: A 822 TYR cc_start: 0.8438 (m-80) cc_final: 0.7965 (m-80) REVERT: A 836 ARG cc_start: 0.7667 (tpp80) cc_final: 0.7426 (tpp-160) outliers start: 41 outliers final: 32 residues processed: 118 average time/residue: 0.0660 time to fit residues: 10.5766 Evaluate side-chains 124 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 HIS ** 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 = 0.4367 r_free = 0.4367 target = 0.202210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.167472 restraints weight = 5725.290| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.22 r_work: 0.3892 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 5769 Z= 0.392 Angle : 2.477 50.505 7855 Z= 1.405 Chirality : 0.428 6.316 871 Planarity : 0.004 0.042 960 Dihedral : 13.011 80.511 887 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 7.58 % Allowed : 28.96 % Favored : 63.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.34), residues: 668 helix: 1.33 (0.29), residues: 326 sheet: -1.68 (0.60), residues: 77 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.010 0.001 TYR A 743 PHE 0.019 0.002 PHE A 884 TRP 0.012 0.001 TRP A 335 HIS 0.007 0.001 HIS A 715 Details of bonding type rmsd/Z covalent geometry : bond 0.01138 / 0.39 ( 5765) covalent geometry : angle 2.13367 / 1.40 ( 7843) hydrogen bonds : bond 0.03473 / 2.18 ( 244) hydrogen bonds : angle 4.59606 / 3.12 ( 708) metal coordination : bond 0.02122 / 1.08 ( 4) metal coordination : angle 32.25193 / 17.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6179 (m-80) cc_final: 0.5862 (t80) REVERT: A 19 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.5813 (t80) REVERT: A 29 MET cc_start: 0.6679 (mtt) cc_final: 0.6088 (mtt) REVERT: A 341 VAL cc_start: 0.8267 (t) cc_final: 0.7932 (t) REVERT: A 528 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7064 (ttpt) REVERT: A 587 HIS cc_start: 0.6950 (m90) cc_final: 0.6454 (m170) REVERT: A 625 SER cc_start: 0.7759 (OUTLIER) cc_final: 0.7500 (m) REVERT: A 664 PHE cc_start: 0.7000 (t80) cc_final: 0.6480 (t80) REVERT: A 665 GLN cc_start: 0.8739 (mm110) cc_final: 0.8299 (pm20) REVERT: A 738 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6383 (pp) REVERT: A 822 TYR cc_start: 0.8454 (m-80) cc_final: 0.7969 (m-80) REVERT: A 836 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7373 (tpp-160) outliers start: 45 outliers final: 35 residues processed: 122 average time/residue: 0.0705 time to fit residues: 11.5334 Evaluate side-chains 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.0010 chunk 19 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 HIS ** 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 = 0.4369 r_free = 0.4369 target = 0.202363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.167760 restraints weight = 5692.910| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.19 r_work: 0.3883 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 5769 Z= 0.391 Angle : 2.473 50.473 7855 Z= 1.404 Chirality : 0.428 6.312 871 Planarity : 0.004 0.041 960 Dihedral : 12.868 80.662 887 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 7.07 % Allowed : 28.96 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.34), residues: 668 helix: 1.40 (0.29), residues: 326 sheet: -1.64 (0.60), residues: 77 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 834 TYR 0.010 0.001 TYR A 247 PHE 0.029 0.002 PHE A 884 TRP 0.012 0.001 TRP A 335 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01136 / 0.39 ( 5765) covalent geometry : angle 2.13027 / 1.40 ( 7843) hydrogen bonds : bond 0.03449 / 2.19 ( 244) hydrogen bonds : angle 4.54292 / 3.07 ( 708) metal coordination : bond 0.02016 / 1.03 ( 4) metal coordination : angle 32.22983 / 17.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6205 (m-80) cc_final: 0.5866 (t80) REVERT: A 19 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.5840 (t80) REVERT: A 29 MET cc_start: 0.6671 (mtt) cc_final: 0.6087 (mtt) REVERT: A 341 VAL cc_start: 0.8252 (t) cc_final: 0.7918 (t) REVERT: A 528 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7063 (ttpt) REVERT: A 587 HIS cc_start: 0.7038 (m90) cc_final: 0.6531 (m170) REVERT: A 625 SER cc_start: 0.7736 (OUTLIER) cc_final: 0.7497 (m) REVERT: A 664 PHE cc_start: 0.7031 (t80) cc_final: 0.6526 (t80) REVERT: A 665 GLN cc_start: 0.8740 (mm110) cc_final: 0.8303 (pm20) REVERT: A 738 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6323 (pp) REVERT: A 822 TYR cc_start: 0.8437 (m-80) cc_final: 0.7950 (m-80) REVERT: A 836 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7304 (tpt170) outliers start: 42 outliers final: 34 residues processed: 120 average time/residue: 0.0698 time to fit residues: 11.3237 Evaluate side-chains 130 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 HIS ** 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 = 0.4371 r_free = 0.4371 target = 0.202577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.167776 restraints weight = 5758.116| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.22 r_work: 0.3893 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 5769 Z= 0.390 Angle : 2.475 50.476 7855 Z= 1.405 Chirality : 0.428 6.312 871 Planarity : 0.004 0.042 960 Dihedral : 12.651 80.726 887 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 6.57 % Allowed : 29.46 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.34), residues: 668 helix: 1.47 (0.29), residues: 326 sheet: -1.61 (0.60), residues: 77 loop : -2.05 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 834 TYR 0.009 0.001 TYR A 742 PHE 0.026 0.002 PHE A 884 TRP 0.012 0.001 TRP A 335 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01136 / 0.39 ( 5765) covalent geometry : angle 2.13198 / 1.40 ( 7843) hydrogen bonds : bond 0.03420 / 2.16 ( 244) hydrogen bonds : angle 4.52726 / 3.06 ( 708) metal coordination : bond 0.02004 / 1.02 ( 4) metal coordination : angle 32.22220 / 17.73 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 0.174 Fit side-chains REVERT: A 16 TYR cc_start: 0.6229 (m-80) cc_final: 0.5876 (t80) REVERT: A 19 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.5811 (t80) REVERT: A 29 MET cc_start: 0.6628 (mtt) cc_final: 0.6032 (mtt) REVERT: A 341 VAL cc_start: 0.8246 (t) cc_final: 0.7913 (t) REVERT: A 528 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7066 (ttpt) REVERT: A 587 HIS cc_start: 0.7053 (m90) cc_final: 0.6539 (m170) REVERT: A 625 SER cc_start: 0.7724 (OUTLIER) cc_final: 0.7487 (m) REVERT: A 664 PHE cc_start: 0.7044 (t80) cc_final: 0.6539 (t80) REVERT: A 665 GLN cc_start: 0.8741 (mm110) cc_final: 0.8294 (pm20) REVERT: A 738 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6335 (pp) REVERT: A 822 TYR cc_start: 0.8435 (m-80) cc_final: 0.7953 (m-80) REVERT: A 836 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7345 (tpt170) outliers start: 39 outliers final: 33 residues processed: 120 average time/residue: 0.0680 time to fit residues: 10.9323 Evaluate side-chains 129 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 273 MET Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 625 SER Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 452 ASN ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.200306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.165160 restraints weight = 5729.790| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.23 r_work: 0.3849 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 5769 Z= 0.408 Angle : 2.490 50.594 7855 Z= 1.411 Chirality : 0.429 6.336 871 Planarity : 0.005 0.071 960 Dihedral : 12.787 80.784 884 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.06 % Allowed : 29.97 % Favored : 63.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.34), residues: 668 helix: 1.42 (0.29), residues: 322 sheet: -1.74 (0.60), residues: 77 loop : -2.07 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 707 TYR 0.019 0.002 TYR A 8 PHE 0.024 0.002 PHE A 884 TRP 0.012 0.001 TRP A 335 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.01168 / 0.41 ( 5765) covalent geometry : angle 2.14778 / 1.41 ( 7843) hydrogen bonds : bond 0.03548 / 2.25 ( 244) hydrogen bonds : angle 4.63423 / 3.14 ( 708) metal coordination : bond 0.02577 / 1.31 ( 4) metal coordination : angle 32.29302 / 17.78 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1351.16 seconds wall clock time: 24 minutes 2.46 seconds (1442.46 seconds total)