Starting phenix.real_space_refine on Thu Sep 10 23:12:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dcq_30639/09_2026/7dcq_30639.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dcq_30639/09_2026/7dcq_30639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dcq_30639/09_2026/7dcq_30639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dcq_30639/09_2026/7dcq_30639.map" model { file = "/net/cci-nas-00/data/ceres_data/7dcq_30639/09_2026/7dcq_30639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dcq_30639/09_2026/7dcq_30639.cif" } resolution = 2.9 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= 0.002 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3316 2.51 5 N 892 2.21 5 O 956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 5197 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5197 Classifications: {'peptide': 653} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 619} Time building chain proxies: 1.31, per 1000 atoms: 0.25 Number of scatterers: 5197 At special positions: 0 Unit cell: (80.1625, 88.1125, 81.4875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 956 8.00 N 892 7.00 C 3316 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: 0.37 Conformation dependent library (CDL) restraints added in 188.7 milliseconds 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1236 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 5 sheets defined 51.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'x' and resid 225 through 227 No H-bonds generated for 'chain 'x' and resid 225 through 227' Processing helix chain 'x' and resid 228 through 239 removed outlier: 3.501A pdb=" N LYS x 238 " --> pdb=" O GLN x 234 " (cutoff:3.500A) Processing helix chain 'x' and resid 251 through 263 removed outlier: 3.500A pdb=" N LEU x 256 " --> pdb=" O LYS x 252 " (cutoff:3.500A) Proline residue: x 257 - end of helix Processing helix chain 'x' and resid 279 through 295 removed outlier: 3.558A pdb=" N ALA x 287 " --> pdb=" O ALA x 283 " (cutoff:3.500A) Processing helix chain 'x' and resid 324 through 329 removed outlier: 3.643A pdb=" N LEU x 328 " --> pdb=" O ASP x 324 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG x 329 " --> pdb=" O GLY x 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 324 through 329' Processing helix chain 'x' and resid 329 through 334 removed outlier: 4.076A pdb=" N THR x 333 " --> pdb=" O ARG x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 347 through 351 Processing helix chain 'x' and resid 352 through 369 removed outlier: 3.693A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE x 365 " --> pdb=" O LEU x 361 " (cutoff:3.500A) Proline residue: x 367 - end of helix Processing helix chain 'x' and resid 382 through 390 removed outlier: 3.598A pdb=" N PHE x 386 " --> pdb=" O ASN x 382 " (cutoff:3.500A) Processing helix chain 'x' and resid 416 through 432 removed outlier: 3.517A pdb=" N ILE x 422 " --> pdb=" O ILE x 418 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR x 423 " --> pdb=" O HIS x 419 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 444 through 463 removed outlier: 3.839A pdb=" N ILE x 448 " --> pdb=" O GLY x 444 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU x 449 " --> pdb=" O GLN x 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU x 457 " --> pdb=" O THR x 453 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE x 458 " --> pdb=" O LYS x 454 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS x 461 " --> pdb=" O GLU x 457 " (cutoff:3.500A) Processing helix chain 'x' and resid 479 through 487 removed outlier: 3.684A pdb=" N LYS x 485 " --> pdb=" O GLU x 481 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE x 487 " --> pdb=" O GLN x 483 " (cutoff:3.500A) Processing helix chain 'x' and resid 542 through 551 Processing helix chain 'x' and resid 566 through 572 Processing helix chain 'x' and resid 580 through 584 Processing helix chain 'x' and resid 587 through 598 Processing helix chain 'x' and resid 612 through 626 Processing helix chain 'x' and resid 636 through 643 Processing helix chain 'x' and resid 648 through 661 removed outlier: 3.698A pdb=" N ALA x 659 " --> pdb=" O LEU x 655 " (cutoff:3.500A) Processing helix chain 'x' and resid 667 through 680 removed outlier: 3.560A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU x 680 " --> pdb=" O SER x 676 " (cutoff:3.500A) Processing helix chain 'x' and resid 681 through 684 Processing helix chain 'x' and resid 688 through 697 removed outlier: 3.587A pdb=" N ALA x 692 " --> pdb=" O GLN x 688 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) Processing helix chain 'x' and resid 702 through 717 removed outlier: 3.609A pdb=" N PHE x 711 " --> pdb=" O TYR x 707 " (cutoff:3.500A) Processing helix chain 'x' and resid 720 through 727 removed outlier: 3.936A pdb=" N CYS x 724 " --> pdb=" O SER x 720 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP x 726 " --> pdb=" O SER x 722 " (cutoff:3.500A) Processing helix chain 'x' and resid 730 through 752 Processing helix chain 'x' and resid 752 through 764 removed outlier: 3.544A pdb=" N LYS x 756 " --> pdb=" O GLY x 752 " (cutoff:3.500A) Processing helix chain 'x' and resid 770 through 783 removed outlier: 3.847A pdb=" N ILE x 775 " --> pdb=" O ILE x 771 " (cutoff:3.500A) Processing helix chain 'x' and resid 813 through 821 removed outlier: 3.621A pdb=" N VAL x 817 " --> pdb=" O SER x 813 " (cutoff:3.500A) Processing helix chain 'x' and resid 852 through 859 removed outlier: 3.643A pdb=" N ILE x 856 " --> pdb=" O GLU x 852 " (cutoff:3.500A) Processing helix chain 'x' and resid 859 through 867 removed outlier: 4.837A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 310 through 311 removed outlier: 6.874A pdb=" N GLY x 303 " --> pdb=" O TYR x 321 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N THR x 323 " --> pdb=" O GLY x 303 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLN x 305 " --> pdb=" O THR x 323 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE x 273 " --> pdb=" O LYS x 320 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET x 322 " --> pdb=" O ILE x 273 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE x 275 " --> pdb=" O MET x 322 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN x 272 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE x 343 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA x 274 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE x 345 " --> pdb=" O ALA x 274 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR x 276 " --> pdb=" O ILE x 345 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER x 378 " --> pdb=" O ILE x 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 405 through 409 removed outlier: 6.115A pdb=" N ASP x 406 " --> pdb=" O CYS x 561 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG x 563 " --> pdb=" O ASP x 406 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS x 408 " --> pdb=" O ARG x 563 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS x 560 " --> pdb=" O ARG x 514 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP x 437 " --> pdb=" O TYR x 515 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE x 517 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU x 439 " --> pdb=" O ILE x 517 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE x 438 " --> pdb=" O VAL x 498 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA x 500 " --> pdb=" O ILE x 438 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL x 440 " --> pdb=" O ALA x 500 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 521 through 527 Processing sheet with id=AA4, first strand: chain 'x' and resid 795 through 797 removed outlier: 4.091A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 808 through 809 removed outlier: 3.557A pdb=" N GLN x 834 " --> pdb=" O ARG x 844 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 615 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: 0.80 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1637 1.34 - 1.45: 649 1.45 - 1.57: 2954 1.57 - 1.69: 1 1.69 - 1.81: 53 Bond restraints: 5294 Sorted by residual: bond pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " ideal model delta sigma weight residual 1.531 1.610 -0.079 3.12e-02 1.03e+03 6.42e+00 bond pdb=" N GLN x 412 " pdb=" CA GLN x 412 " ideal model delta sigma weight residual 1.455 1.470 -0.015 7.00e-03 2.04e+04 4.45e+00 bond pdb=" C GLN x 412 " pdb=" N PRO x 413 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.32e-02 5.74e+03 2.83e+00 bond pdb=" CB ARG x 584 " pdb=" CG ARG x 584 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.72e+00 bond pdb=" CA LEU x 411 " pdb=" C LEU x 411 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.30e-02 5.92e+03 2.56e+00 ... (remaining 5289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6984 2.57 - 5.14: 143 5.14 - 7.71: 25 7.71 - 10.28: 5 10.28 - 12.86: 2 Bond angle restraints: 7159 Sorted by residual: angle pdb=" N LEU x 411 " pdb=" CA LEU x 411 " pdb=" C LEU x 411 " ideal model delta sigma weight residual 111.28 120.48 -9.20 1.09e+00 8.42e-01 7.12e+01 angle pdb=" N GLU x 414 " pdb=" CA GLU x 414 " pdb=" C GLU x 414 " ideal model delta sigma weight residual 107.62 120.48 -12.86 1.97e+00 2.58e-01 4.26e+01 angle pdb=" C GLN x 412 " pdb=" N PRO x 413 " pdb=" CA PRO x 413 " ideal model delta sigma weight residual 119.76 113.74 6.02 1.00e+00 1.00e+00 3.62e+01 angle pdb=" C THR x 266 " pdb=" N ASP x 267 " pdb=" CA ASP x 267 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.92e+01 angle pdb=" C THR x 838 " pdb=" N SER x 839 " pdb=" CA SER x 839 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 ... (remaining 7154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.73: 3074 14.73 - 29.45: 131 29.45 - 44.18: 52 44.18 - 58.90: 5 58.90 - 73.63: 5 Dihedral angle restraints: 3267 sinusoidal: 1360 harmonic: 1907 Sorted by residual: dihedral pdb=" C ASP x 391 " pdb=" N ASP x 391 " pdb=" CA ASP x 391 " pdb=" CB ASP x 391 " ideal model delta harmonic sigma weight residual -122.60 -134.75 12.15 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" N ASP x 391 " pdb=" C ASP x 391 " pdb=" CA ASP x 391 " pdb=" CB ASP x 391 " ideal model delta harmonic sigma weight residual 122.80 134.26 -11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" CA ILE x 862 " pdb=" C ILE x 862 " pdb=" N PHE x 863 " pdb=" CA PHE x 863 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 737 0.092 - 0.183: 86 0.183 - 0.275: 4 0.275 - 0.366: 4 0.366 - 0.458: 1 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ASP x 391 " pdb=" N ASP x 391 " pdb=" C ASP x 391 " pdb=" CB ASP x 391 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB THR x 585 " pdb=" CA THR x 585 " pdb=" OG1 THR x 585 " pdb=" CG2 THR x 585 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA GLU x 414 " pdb=" N GLU x 414 " pdb=" C GLU x 414 " pdb=" CB GLU x 414 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 829 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE x 605 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO x 606 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO x 606 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO x 606 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU x 434 " 0.047 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO x 435 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO x 435 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO x 435 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR x 409 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C TYR x 409 " 0.044 2.00e-02 2.50e+03 pdb=" O TYR x 409 " -0.017 2.00e-02 2.50e+03 pdb=" N THR x 410 " -0.015 2.00e-02 2.50e+03 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1785 2.88 - 3.39: 4953 3.39 - 3.89: 8352 3.89 - 4.40: 9688 4.40 - 4.90: 16503 Nonbonded interactions: 41281 Sorted by model distance: nonbonded pdb=" OE1 GLU x 644 " pdb=" NZ LYS x 750 " model vdw 2.378 3.120 nonbonded pdb=" O LEU x 337 " pdb=" NH1 ARG x 369 " model vdw 2.383 3.120 nonbonded pdb=" OE1 GLN x 834 " pdb=" NH2 ARG x 844 " model vdw 2.386 3.120 nonbonded pdb=" OG1 THR x 266 " pdb=" N ASP x 267 " model vdw 2.397 3.120 nonbonded pdb=" OE2 GLU x 449 " pdb=" OH TYR x 475 " model vdw 2.397 3.040 ... (remaining 41276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.060 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.850 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.006 0.079 5294 Z= 0.242 Angle : 0.949 12.856 7159 Z= 0.516 Chirality : 0.061 0.458 832 Planarity : 0.008 0.072 909 Dihedral : 10.613 73.626 2031 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.85 % Allowed : 2.73 % Favored : 96.42 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.03 % 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: -3.49 (0.26), residues: 651 helix: -3.36 (0.17), residues: 277 sheet: -0.46 (0.45), residues: 123 loop : -1.75 (0.34), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG x 289 TYR 0.023 0.003 TYR x 321 PHE 0.028 0.003 PHE x 863 TRP 0.029 0.004 TRP x 723 HIS 0.004 0.001 HIS x 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.24 ( 5294) covalent geometry : angle 0.94898 / 0.52 ( 7159) hydrogen bonds : bond 0.30278 / 19.39 ( 213) hydrogen bonds : angle 8.56197 / 5.79 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 454 LYS cc_start: 0.7709 (tptp) cc_final: 0.7309 (tttt) REVERT: x 494 CYS cc_start: 0.7814 (m) cc_final: 0.7509 (m) outliers start: 5 outliers final: 1 residues processed: 150 average time/residue: 0.6115 time to fit residues: 95.0593 Evaluate side-chains 79 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 585 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0170 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 295 ASN x 408 HIS ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 477 ASN x 630 ASN x 725 GLN x 743 GLN x 834 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131067 restraints weight = 6899.404| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.21 r_work: 0.3572 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5294 Z= 0.118 Angle : 0.605 7.347 7159 Z= 0.309 Chirality : 0.044 0.186 832 Planarity : 0.006 0.065 909 Dihedral : 4.971 40.366 707 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.39 % Allowed : 14.82 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.35 (0.30), residues: 651 helix: -0.78 (0.26), residues: 292 sheet: -0.48 (0.45), residues: 121 loop : -1.01 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG x 401 TYR 0.008 0.001 TYR x 832 PHE 0.017 0.002 PHE x 396 TRP 0.015 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 5294) covalent geometry : angle 0.60469 / 0.31 ( 7159) hydrogen bonds : bond 0.03667 / 2.34 ( 213) hydrogen bonds : angle 4.42493 / 2.93 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: x 301 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: x 305 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: x 320 LYS cc_start: 0.8609 (ptmt) cc_final: 0.8291 (ptpt) REVERT: x 427 GLN cc_start: 0.8035 (tp40) cc_final: 0.7769 (tp40) REVERT: x 454 LYS cc_start: 0.7583 (tptp) cc_final: 0.7104 (tttt) REVERT: x 483 GLN cc_start: 0.7415 (mm110) cc_final: 0.7128 (mm110) REVERT: x 700 VAL cc_start: 0.7080 (t) cc_final: 0.6861 (p) REVERT: x 762 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7109 (ptm) REVERT: x 763 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7343 (tttp) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.5463 time to fit residues: 61.4310 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 342 CYS Chi-restraints excluded: chain x residue 382 ASN Chi-restraints excluded: chain x residue 443 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 762 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 630 ASN x 834 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129421 restraints weight = 6793.593| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.19 r_work: 0.3548 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5294 Z= 0.114 Angle : 0.556 6.160 7159 Z= 0.281 Chirality : 0.043 0.174 832 Planarity : 0.005 0.057 909 Dihedral : 4.599 35.179 707 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.09 % Allowed : 15.50 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.27 (0.32), residues: 651 helix: 0.43 (0.29), residues: 293 sheet: 0.05 (0.47), residues: 121 loop : -0.95 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 401 TYR 0.009 0.001 TYR x 832 PHE 0.014 0.002 PHE x 863 TRP 0.008 0.001 TRP x 723 HIS 0.002 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 5294) covalent geometry : angle 0.55605 / 0.28 ( 7159) hydrogen bonds : bond 0.03382 / 2.10 ( 213) hydrogen bonds : angle 4.01333 / 2.64 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.217 Fit side-chains REVERT: x 301 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.6771 (mt-10) REVERT: x 305 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: x 320 LYS cc_start: 0.8659 (ptmt) cc_final: 0.8297 (ptpt) REVERT: x 427 GLN cc_start: 0.8017 (tp40) cc_final: 0.7694 (tp-100) REVERT: x 454 LYS cc_start: 0.7760 (tptp) cc_final: 0.7337 (tttt) REVERT: x 483 GLN cc_start: 0.7359 (mm110) cc_final: 0.7159 (mm110) REVERT: x 762 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.7101 (ptm) REVERT: x 767 ILE cc_start: 0.6059 (OUTLIER) cc_final: 0.5607 (mt) outliers start: 24 outliers final: 9 residues processed: 101 average time/residue: 0.5225 time to fit residues: 55.1299 Evaluate side-chains 91 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 342 CYS Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.4122 > 50:) chunk 28 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 239 ASN ** x 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 630 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129140 restraints weight = 6860.250| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.19 r_work: 0.3551 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5294 Z= 0.124 Angle : 0.549 6.395 7159 Z= 0.277 Chirality : 0.044 0.193 832 Planarity : 0.005 0.054 909 Dihedral : 4.640 40.812 707 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.77 % Allowed : 15.33 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.20 (0.33), residues: 651 helix: 1.10 (0.31), residues: 293 sheet: -0.11 (0.48), residues: 122 loop : -0.88 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG x 844 TYR 0.010 0.001 TYR x 795 PHE 0.014 0.002 PHE x 426 TRP 0.007 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 5294) covalent geometry : angle 0.54905 / 0.28 ( 7159) hydrogen bonds : bond 0.03185 / 1.98 ( 213) hydrogen bonds : angle 3.82638 / 2.52 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.207 Fit side-chains REVERT: x 305 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: x 320 LYS cc_start: 0.8637 (ptmt) cc_final: 0.8277 (ptpt) REVERT: x 422 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7538 (pt) REVERT: x 427 GLN cc_start: 0.8010 (tp40) cc_final: 0.7668 (tp-100) REVERT: x 454 LYS cc_start: 0.7707 (tptp) cc_final: 0.7283 (tttt) REVERT: x 483 GLN cc_start: 0.7388 (mm110) cc_final: 0.7029 (mm110) REVERT: x 604 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8518 (tptm) REVERT: x 762 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7080 (ptm) REVERT: x 764 ILE cc_start: 0.7889 (tp) cc_final: 0.7484 (pp) REVERT: x 767 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5679 (mt) outliers start: 28 outliers final: 11 residues processed: 97 average time/residue: 0.5273 time to fit residues: 53.5009 Evaluate side-chains 90 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 685 PHE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 796 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130479 restraints weight = 6917.427| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.20 r_work: 0.3562 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5294 Z= 0.111 Angle : 0.542 6.606 7159 Z= 0.274 Chirality : 0.043 0.185 832 Planarity : 0.004 0.052 909 Dihedral : 4.493 37.864 707 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.41 % Allowed : 16.87 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.43 (0.34), residues: 651 helix: 1.45 (0.31), residues: 294 sheet: -0.19 (0.48), residues: 120 loop : -0.88 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 401 TYR 0.009 0.001 TYR x 832 PHE 0.015 0.002 PHE x 816 TRP 0.005 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 5294) covalent geometry : angle 0.54217 / 0.27 ( 7159) hydrogen bonds : bond 0.02912 / 1.79 ( 213) hydrogen bonds : angle 3.71405 / 2.43 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.211 Fit side-chains REVERT: x 232 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7792 (mt) REVERT: x 305 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: x 320 LYS cc_start: 0.8641 (ptmt) cc_final: 0.8264 (ptpt) REVERT: x 427 GLN cc_start: 0.8021 (tp40) cc_final: 0.7748 (tp-100) REVERT: x 454 LYS cc_start: 0.7661 (tptp) cc_final: 0.7289 (tttt) REVERT: x 577 MET cc_start: 0.8038 (tpt) cc_final: 0.7763 (tpt) REVERT: x 762 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7077 (ptm) REVERT: x 764 ILE cc_start: 0.7898 (tp) cc_final: 0.7535 (pp) REVERT: x 767 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5662 (mt) outliers start: 20 outliers final: 8 residues processed: 94 average time/residue: 0.4847 time to fit residues: 47.7678 Evaluate side-chains 84 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 480 GLN x 630 ASN x 727 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127123 restraints weight = 6881.518| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.21 r_work: 0.3514 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5294 Z= 0.123 Angle : 0.557 6.609 7159 Z= 0.278 Chirality : 0.044 0.206 832 Planarity : 0.004 0.052 909 Dihedral : 4.482 38.365 707 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.58 % Allowed : 17.04 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.56 (0.34), residues: 651 helix: 1.62 (0.31), residues: 292 sheet: -0.24 (0.48), residues: 120 loop : -0.80 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG x 844 TYR 0.009 0.001 TYR x 832 PHE 0.015 0.002 PHE x 816 TRP 0.006 0.001 TRP x 723 HIS 0.004 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 ( 5294) covalent geometry : angle 0.55728 / 0.28 ( 7159) hydrogen bonds : bond 0.03047 / 1.89 ( 213) hydrogen bonds : angle 3.69288 / 2.41 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.186 Fit side-chains REVERT: x 232 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7804 (mt) REVERT: x 422 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7547 (pt) REVERT: x 427 GLN cc_start: 0.8023 (tp40) cc_final: 0.7759 (tp-100) REVERT: x 454 LYS cc_start: 0.7571 (tptp) cc_final: 0.7158 (tttt) REVERT: x 689 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7551 (ptmt) REVERT: x 762 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7097 (ptm) REVERT: x 764 ILE cc_start: 0.7991 (tp) cc_final: 0.7598 (pp) REVERT: x 767 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5713 (mt) outliers start: 21 outliers final: 11 residues processed: 88 average time/residue: 0.4684 time to fit residues: 43.3246 Evaluate side-chains 89 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 305 GLN Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 588 SER Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 689 LYS Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 762 MET Chi-restraints excluded: chain x residue 767 ILE Chi-restraints excluded: chain x residue 798 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 429 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 = 0.3917 r_free = 0.3917 target = 0.151165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129744 restraints weight = 6785.102| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.20 r_work: 0.3553 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5294 Z= 0.098 Angle : 0.536 8.147 7159 Z= 0.264 Chirality : 0.043 0.183 832 Planarity : 0.004 0.050 909 Dihedral : 4.322 37.124 707 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.92 % Allowed : 16.87 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.78 (0.34), residues: 651 helix: 1.87 (0.32), residues: 292 sheet: -0.17 (0.49), residues: 119 loop : -0.78 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG x 289 TYR 0.008 0.001 TYR x 832 PHE 0.018 0.001 PHE x 816 TRP 0.003 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 5294) covalent geometry : angle 0.53589 / 0.26 ( 7159) hydrogen bonds : bond 0.02701 / 1.68 ( 213) hydrogen bonds : angle 3.60939 / 2.35 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.213 Fit side-chains REVERT: x 221 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7698 (mttt) REVERT: x 232 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7849 (mt) REVERT: x 301 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: x 427 GLN cc_start: 0.7971 (tp40) cc_final: 0.7742 (tp-100) REVERT: x 454 LYS cc_start: 0.7522 (tptp) cc_final: 0.7173 (tttt) REVERT: x 564 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8288 (mm) REVERT: x 689 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7435 (ptmt) REVERT: x 767 ILE cc_start: 0.6097 (OUTLIER) cc_final: 0.5622 (mt) outliers start: 23 outliers final: 8 residues processed: 93 average time/residue: 0.4885 time to fit residues: 47.6163 Evaluate side-chains 87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 301 GLU Chi-restraints excluded: chain x residue 322 MET Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 564 ILE Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 689 LYS Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Chi-restraints excluded: chain x residue 798 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 429 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 = 0.3881 r_free = 0.3881 target = 0.148134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126901 restraints weight = 6938.415| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.21 r_work: 0.3510 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5294 Z= 0.138 Angle : 0.573 7.749 7159 Z= 0.284 Chirality : 0.045 0.233 832 Planarity : 0.004 0.051 909 Dihedral : 4.469 38.713 707 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.92 % Allowed : 18.40 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.72 (0.34), residues: 651 helix: 1.76 (0.31), residues: 292 sheet: -0.21 (0.49), residues: 119 loop : -0.71 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 289 TYR 0.010 0.002 TYR x 475 PHE 0.018 0.002 PHE x 816 TRP 0.006 0.001 TRP x 723 HIS 0.004 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 5294) covalent geometry : angle 0.57342 / 0.28 ( 7159) hydrogen bonds : bond 0.03115 / 1.94 ( 213) hydrogen bonds : angle 3.68002 / 2.40 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.172 Fit side-chains REVERT: x 221 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7748 (mttt) REVERT: x 232 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7879 (mt) REVERT: x 422 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7572 (pt) REVERT: x 427 GLN cc_start: 0.8000 (tp40) cc_final: 0.7756 (tp-100) REVERT: x 454 LYS cc_start: 0.7604 (tptp) cc_final: 0.7212 (tttt) REVERT: x 762 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7113 (ptm) REVERT: x 764 ILE cc_start: 0.7980 (tp) cc_final: 0.7629 (pp) REVERT: x 767 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5712 (mt) outliers start: 23 outliers final: 8 residues processed: 89 average time/residue: 0.4865 time to fit residues: 45.3923 Evaluate side-chains 84 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 762 MET Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 429 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 = 0.3901 r_free = 0.3901 target = 0.149774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128585 restraints weight = 6880.206| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.20 r_work: 0.3535 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5294 Z= 0.110 Angle : 0.556 8.559 7159 Z= 0.273 Chirality : 0.044 0.218 832 Planarity : 0.004 0.049 909 Dihedral : 4.388 37.764 707 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.73 % Allowed : 19.93 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.82 (0.34), residues: 651 helix: 1.89 (0.32), residues: 292 sheet: -0.23 (0.49), residues: 119 loop : -0.70 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 289 TYR 0.009 0.001 TYR x 832 PHE 0.014 0.002 PHE x 426 TRP 0.004 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 5294) covalent geometry : angle 0.55563 / 0.27 ( 7159) hydrogen bonds : bond 0.02887 / 1.79 ( 213) hydrogen bonds : angle 3.60379 / 2.36 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.225 Fit side-chains REVERT: x 221 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7729 (mttt) REVERT: x 232 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7890 (mt) REVERT: x 422 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7551 (pt) REVERT: x 427 GLN cc_start: 0.7974 (tp40) cc_final: 0.7739 (tp-100) REVERT: x 454 LYS cc_start: 0.7559 (tptp) cc_final: 0.7187 (tttt) REVERT: x 767 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5665 (mt) outliers start: 16 outliers final: 7 residues processed: 83 average time/residue: 0.5109 time to fit residues: 44.2793 Evaluate side-chains 82 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 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 = 0.3917 r_free = 0.3917 target = 0.151114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129641 restraints weight = 6914.813| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.22 r_work: 0.3546 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5294 Z= 0.105 Angle : 0.553 9.479 7159 Z= 0.271 Chirality : 0.044 0.211 832 Planarity : 0.004 0.049 909 Dihedral : 4.341 37.804 707 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.90 % Allowed : 20.10 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.88 (0.34), residues: 651 helix: 1.94 (0.32), residues: 293 sheet: -0.23 (0.49), residues: 119 loop : -0.65 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 289 TYR 0.009 0.001 TYR x 832 PHE 0.022 0.002 PHE x 816 TRP 0.004 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.10 ( 5294) covalent geometry : angle 0.55317 / 0.27 ( 7159) hydrogen bonds : bond 0.02785 / 1.74 ( 213) hydrogen bonds : angle 3.59841 / 2.35 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1302 Ramachandran restraints generated. 651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: x 221 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7717 (mttt) REVERT: x 232 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7888 (mt) REVERT: x 347 GLU cc_start: 0.8529 (mp0) cc_final: 0.8145 (mm-30) REVERT: x 422 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7547 (pt) REVERT: x 427 GLN cc_start: 0.7947 (tp40) cc_final: 0.7714 (tp-100) REVERT: x 454 LYS cc_start: 0.7509 (tptp) cc_final: 0.7153 (tttt) REVERT: x 469 MET cc_start: 0.7552 (tmm) cc_final: 0.6047 (ttm) REVERT: x 564 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8193 (mm) REVERT: x 767 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5586 (mt) outliers start: 17 outliers final: 10 residues processed: 85 average time/residue: 0.5395 time to fit residues: 47.9316 Evaluate side-chains 86 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 221 LYS Chi-restraints excluded: chain x residue 232 LEU Chi-restraints excluded: chain x residue 281 VAL Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 355 THR Chi-restraints excluded: chain x residue 382 ASN Chi-restraints excluded: chain x residue 422 ILE Chi-restraints excluded: chain x residue 531 THR Chi-restraints excluded: chain x residue 564 ILE Chi-restraints excluded: chain x residue 576 LEU Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 608 MET Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 720 SER Chi-restraints excluded: chain x residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... x 382 ASN ** x 429 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 = 0.3918 r_free = 0.3918 target = 0.151179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129691 restraints weight = 6949.572| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.23 r_work: 0.3548 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 5294 Z= 0.202 Angle : 1.065 59.156 7159 Z= 0.632 Chirality : 0.058 1.090 832 Planarity : 0.006 0.124 909 Dihedral : 4.311 37.830 707 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.90 % Allowed : 20.10 % Favored : 77.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 3.03 % 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: 0.86 (0.34), residues: 651 helix: 1.94 (0.32), residues: 293 sheet: -0.23 (0.49), residues: 119 loop : -0.69 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG x 844 TYR 0.010 0.001 TYR x 340 PHE 0.015 0.002 PHE x 816 TRP 0.004 0.001 TRP x 723 HIS 0.003 0.001 HIS x 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.20 ( 5294) covalent geometry : angle 1.06544 / 0.63 ( 7159) hydrogen bonds : bond 0.02801 / 1.75 ( 213) hydrogen bonds : angle 3.59906 / 2.35 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.68 seconds wall clock time: 33 minutes 59.93 seconds (2039.93 seconds total)