Starting phenix.real_space_refine on Fri Sep 11 06:36:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.cif" model { file = "/net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9e_9013/09_2026/6e9e_9013.map" } resolution = 3.4 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= -0.005 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 30 5.16 5 C 4985 2.51 5 N 1401 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8163 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1088 Classifications: {'RNAv2': 51} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 19} Link IDs: {'rna2p': 12, 'rna3p': 38} Chain: "A" Number of atoms: 7074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 7074 Classifications: {'peptide': 863} Link IDs: {'PTRANS': 13, 'TRANS': 849} Chain breaks: 5 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.61, per 1000 atoms: 0.20 Number of scatterers: 8163 At special positions: 0 Unit cell: (102.7, 85.32, 101.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 51 15.00 Mg 1 11.99 O 1695 8.00 N 1401 7.00 C 4985 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: 0.69 Conformation dependent library (CDL) restraints added in 235.3 milliseconds 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1660 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 63.3% alpha, 2.3% beta 2 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.782A pdb=" N LEU A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 removed outlier: 3.652A pdb=" N GLN A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A 186 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.565A pdb=" N GLU A 234 " --> pdb=" O LYS A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 237 through 252 Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.024A pdb=" N LEU A 256 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.542A pdb=" N LEU A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 4.016A pdb=" N PHE A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.968A pdb=" N VAL A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 3.503A pdb=" N GLU A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.707A pdb=" N ILE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.849A pdb=" N ASN A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 3.796A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 422 removed outlier: 3.785A pdb=" N MET A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 436 removed outlier: 3.898A pdb=" N SER A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 458 removed outlier: 3.503A pdb=" N LYS A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.613A pdb=" N LYS A 475 " --> pdb=" O GLY A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.827A pdb=" N LYS A 491 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 3.544A pdb=" N TYR A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 543 removed outlier: 3.742A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 520 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 536 " --> pdb=" O ASN A 532 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.751A pdb=" N PHE A 556 " --> pdb=" O TYR A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 removed outlier: 3.925A pdb=" N ALA A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 572 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 593 removed outlier: 3.846A pdb=" N TYR A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 removed outlier: 3.616A pdb=" N GLU A 606 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.954A pdb=" N ARG A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 659 removed outlier: 3.523A pdb=" N ILE A 655 " --> pdb=" O ASN A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 673 through 685 removed outlier: 3.623A pdb=" N ARG A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 683 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.715A pdb=" N SER A 714 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 779 removed outlier: 3.624A pdb=" N GLU A 732 " --> pdb=" O THR A 728 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 741 " --> pdb=" O ASN A 737 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A 748 " --> pdb=" O TYR A 744 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 761 " --> pdb=" O ASN A 757 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 762 " --> pdb=" O VAL A 758 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 764 " --> pdb=" O ALA A 760 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 765 " --> pdb=" O ARG A 761 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 799 removed outlier: 3.584A pdb=" N MET A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 818 removed outlier: 4.077A pdb=" N ALA A 816 " --> pdb=" O ASP A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 838 Processing helix chain 'A' and resid 841 through 853 removed outlier: 3.718A pdb=" N VAL A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 removed outlier: 3.542A pdb=" N ASN A 860 " --> pdb=" O ASN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 888 removed outlier: 3.977A pdb=" N GLN A 883 " --> pdb=" O HIS A 879 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 886 " --> pdb=" O ILE A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 3.625A pdb=" N HIS A 909 " --> pdb=" O LYS A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 921 removed outlier: 3.858A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.627A pdb=" N TYR A 931 " --> pdb=" O ASN A 927 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 3.504A pdb=" N GLU A 100 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 266 301 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.91 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: 2434 1.34 - 1.46: 1608 1.46 - 1.57: 4221 1.57 - 1.69: 101 1.69 - 1.81: 47 Bond restraints: 8411 Sorted by residual: bond pdb=" C THR A 922 " pdb=" N PRO A 923 " ideal model delta sigma weight residual 1.335 1.386 -0.051 1.19e-02 7.06e+03 1.84e+01 bond pdb=" N VAL A 193 " pdb=" CA VAL A 193 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.22e-02 6.72e+03 7.18e+00 bond pdb=" CA SER A 437 " pdb=" CB SER A 437 " ideal model delta sigma weight residual 1.534 1.491 0.043 1.72e-02 3.38e+03 6.29e+00 bond pdb=" N LYS A 439 " pdb=" CA LYS A 439 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.29e-02 6.01e+03 5.94e+00 bond pdb=" N ILE A 190 " pdb=" CA ILE A 190 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.19e-02 7.06e+03 5.60e+00 ... (remaining 8406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 10891 1.61 - 3.23: 557 3.23 - 4.84: 96 4.84 - 6.45: 16 6.45 - 8.07: 4 Bond angle restraints: 11564 Sorted by residual: angle pdb=" C VAL A 193 " pdb=" N TYR A 194 " pdb=" CA TYR A 194 " ideal model delta sigma weight residual 120.72 128.79 -8.07 1.67e+00 3.59e-01 2.33e+01 angle pdb=" N LEU A 350 " pdb=" CA LEU A 350 " pdb=" C LEU A 350 " ideal model delta sigma weight residual 112.45 107.48 4.97 1.39e+00 5.18e-01 1.28e+01 angle pdb=" C CYS A 661 " pdb=" N LYS A 662 " pdb=" CA LYS A 662 " ideal model delta sigma weight residual 120.58 124.80 -4.22 1.32e+00 5.74e-01 1.02e+01 angle pdb=" CA ILE A 190 " pdb=" C ILE A 190 " pdb=" O ILE A 190 " ideal model delta sigma weight residual 120.95 117.75 3.20 1.04e+00 9.25e-01 9.44e+00 angle pdb=" N LYS A 189 " pdb=" CA LYS A 189 " pdb=" C LYS A 189 " ideal model delta sigma weight residual 111.03 107.71 3.32 1.11e+00 8.12e-01 8.93e+00 ... (remaining 11559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 4631 16.05 - 32.10: 242 32.10 - 48.16: 59 48.16 - 64.21: 55 64.21 - 80.26: 16 Dihedral angle restraints: 5003 sinusoidal: 2438 harmonic: 2565 Sorted by residual: dihedral pdb=" C4' A B 12 " pdb=" C3' A B 12 " pdb=" C2' A B 12 " pdb=" C1' A B 12 " ideal model delta sinusoidal sigma weight residual 36.34 -37.62 73.97 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' A B 50 " pdb=" C3' A B 50 " pdb=" C2' A B 50 " pdb=" C1' A B 50 " ideal model delta sinusoidal sigma weight residual 36.34 -37.41 73.75 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A B 13 " pdb=" C3' A B 13 " pdb=" C2' A B 13 " pdb=" C1' A B 13 " ideal model delta sinusoidal sigma weight residual 36.34 -36.36 72.70 1 3.10e+00 1.04e-01 7.02e+02 ... (remaining 5000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1023 0.060 - 0.119: 204 0.119 - 0.179: 16 0.179 - 0.239: 41 0.239 - 0.298: 33 Chirality restraints: 1317 Sorted by residual: chirality pdb=" C2' G B 22 " pdb=" C3' G B 22 " pdb=" O2' G B 22 " pdb=" C1' G B 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' A B 50 " pdb=" C3' A B 50 " pdb=" O2' A B 50 " pdb=" C1' A B 50 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C2' G B 36 " pdb=" C3' G B 36 " pdb=" O2' G B 36 " pdb=" C1' G B 36 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1314 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 348 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C GLN A 348 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN A 348 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 349 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 135 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A 136 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 916 " 0.015 2.00e-02 2.50e+03 1.36e-02 3.25e+00 pdb=" CG PHE A 916 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 916 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 916 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 916 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 916 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 916 " 0.004 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 99 2.61 - 3.18: 7326 3.18 - 3.75: 11538 3.75 - 4.33: 17581 4.33 - 4.90: 28017 Nonbonded interactions: 64561 Sorted by model distance: nonbonded pdb=" OP1 U B 41 " pdb=" OG SER A 575 " model vdw 2.037 3.040 nonbonded pdb=" OE2 GLU A 361 " pdb=" NZ LYS A 488 " model vdw 2.198 3.120 nonbonded pdb=" O VAL A 724 " pdb=" NH2 ARG A 735 " model vdw 2.214 3.120 nonbonded pdb=" OP1 A B 37 " pdb=" NZ LYS A 753 " model vdw 2.226 3.120 nonbonded pdb=" O4 U B 43 " pdb=" NZ LYS A 475 " model vdw 2.227 3.120 ... (remaining 64556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.100 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.040 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.062 8411 Z= 0.261 Angle : 0.834 8.068 11564 Z= 0.449 Chirality : 0.072 0.298 1317 Planarity : 0.003 0.046 1290 Dihedral : 13.280 80.258 3343 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.26 % Allowed : 2.32 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.22), residues: 851 helix: -3.69 (0.15), residues: 511 sheet: -3.80 (0.86), residues: 23 loop : -2.12 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 666 TYR 0.022 0.002 TYR A 912 PHE 0.031 0.002 PHE A 916 TRP 0.016 0.003 TRP A 455 HIS 0.005 0.002 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.26 ( 8411) covalent geometry : angle 0.83414 / 0.45 (11564) hydrogen bonds : bond 0.30175 / 15.40 ( 305) hydrogen bonds : angle 9.26567 / 3.72 ( 876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.228 Fit side-chains REVERT: A 191 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9183 (mt) REVERT: A 605 ILE cc_start: 0.8440 (pt) cc_final: 0.8144 (mt) REVERT: A 685 CYS cc_start: 0.7131 (t) cc_final: 0.6913 (t) REVERT: A 703 ASP cc_start: 0.6749 (p0) cc_final: 0.6388 (p0) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.1261 time to fit residues: 23.3909 Evaluate side-chains 53 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0040 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 ASN A 792 ASN A 864 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.081956 restraints weight = 17483.221| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.07 r_work: 0.2907 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8411 Z= 0.152 Angle : 0.825 13.828 11564 Z= 0.379 Chirality : 0.067 0.649 1317 Planarity : 0.003 0.032 1290 Dihedral : 13.635 151.988 1566 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.39 % Allowed : 6.31 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.25), residues: 851 helix: -1.79 (0.20), residues: 518 sheet: -3.61 (0.83), residues: 14 loop : -1.69 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 138 TYR 0.014 0.001 TYR A 880 PHE 0.011 0.001 PHE A 667 TRP 0.012 0.002 TRP A 829 HIS 0.002 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 8411) covalent geometry : angle 0.82528 / 0.38 (11564) hydrogen bonds : bond 0.06614 / 3.37 ( 305) hydrogen bonds : angle 4.59540 / 1.80 ( 876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.170 Fit side-chains REVERT: A 156 MET cc_start: 0.8250 (mmm) cc_final: 0.8031 (mmt) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 0.0890 time to fit residues: 8.9544 Evaluate side-chains 40 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 720 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.078634 restraints weight = 17366.671| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.15 r_work: 0.2849 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8411 Z= 0.112 Angle : 0.638 10.904 11564 Z= 0.300 Chirality : 0.054 0.598 1317 Planarity : 0.003 0.026 1290 Dihedral : 13.888 179.003 1564 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.90 % Allowed : 7.34 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.27), residues: 851 helix: -0.71 (0.21), residues: 524 sheet: -2.22 (0.87), residues: 27 loop : -1.30 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 138 TYR 0.011 0.001 TYR A 880 PHE 0.011 0.001 PHE A 916 TRP 0.010 0.002 TRP A 829 HIS 0.003 0.001 HIS A 767 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8411) covalent geometry : angle 0.63810 / 0.30 (11564) hydrogen bonds : bond 0.04994 / 2.54 ( 305) hydrogen bonds : angle 3.87027 / 1.53 ( 876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7632 (tm-30) REVERT: A 470 ASP cc_start: 0.8179 (p0) cc_final: 0.7780 (t0) outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 0.0989 time to fit residues: 8.8071 Evaluate side-chains 46 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 909 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077530 restraints weight = 17678.388| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.18 r_work: 0.2835 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8411 Z= 0.104 Angle : 0.584 8.365 11564 Z= 0.276 Chirality : 0.052 0.604 1317 Planarity : 0.002 0.024 1290 Dihedral : 13.800 179.537 1562 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.64 % Allowed : 7.98 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.28), residues: 851 helix: -0.13 (0.22), residues: 527 sheet: -1.63 (0.87), residues: 32 loop : -1.08 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 138 TYR 0.008 0.001 TYR A 920 PHE 0.010 0.001 PHE A 916 TRP 0.009 0.002 TRP A 829 HIS 0.003 0.001 HIS A 767 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 8411) covalent geometry : angle 0.58397 / 0.28 (11564) hydrogen bonds : bond 0.04439 / 2.26 ( 305) hydrogen bonds : angle 3.57656 / 1.43 ( 876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.290 Fit side-chains REVERT: A 334 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 470 ASP cc_start: 0.8093 (p0) cc_final: 0.7804 (t0) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.0875 time to fit residues: 7.2623 Evaluate side-chains 44 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.086943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.069849 restraints weight = 17589.753| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.15 r_work: 0.2685 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8411 Z= 0.161 Angle : 0.639 8.347 11564 Z= 0.304 Chirality : 0.055 0.522 1317 Planarity : 0.003 0.026 1290 Dihedral : 13.852 179.168 1562 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.77 % Allowed : 9.01 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.28), residues: 851 helix: 0.00 (0.22), residues: 533 sheet: -1.67 (0.89), residues: 34 loop : -1.15 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 930 TYR 0.015 0.001 TYR A 920 PHE 0.021 0.001 PHE A 916 TRP 0.011 0.002 TRP A 829 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 8411) covalent geometry : angle 0.63892 / 0.30 (11564) hydrogen bonds : bond 0.05018 / 2.57 ( 305) hydrogen bonds : angle 3.75980 / 1.48 ( 876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.304 Fit side-chains REVERT: A 334 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8460 (tm-30) REVERT: A 470 ASP cc_start: 0.8152 (p0) cc_final: 0.7819 (t0) REVERT: A 685 CYS cc_start: 0.7185 (t) cc_final: 0.6837 (t) REVERT: A 715 ASP cc_start: 0.8208 (t0) cc_final: 0.7932 (t0) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.0801 time to fit residues: 6.2045 Evaluate side-chains 40 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.070096 restraints weight = 17374.031| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.13 r_work: 0.2693 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8411 Z= 0.140 Angle : 0.616 8.326 11564 Z= 0.292 Chirality : 0.053 0.507 1317 Planarity : 0.002 0.021 1290 Dihedral : 13.797 179.002 1562 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.29 % Allowed : 9.52 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.28), residues: 851 helix: 0.23 (0.23), residues: 533 sheet: -1.55 (0.92), residues: 34 loop : -0.95 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 930 TYR 0.012 0.001 TYR A 920 PHE 0.017 0.001 PHE A 916 TRP 0.011 0.002 TRP A 829 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8411) covalent geometry : angle 0.61560 / 0.29 (11564) hydrogen bonds : bond 0.04621 / 2.37 ( 305) hydrogen bonds : angle 3.64317 / 1.44 ( 876) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.180 Fit side-chains REVERT: A 334 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 470 ASP cc_start: 0.8143 (p0) cc_final: 0.7820 (t0) REVERT: A 685 CYS cc_start: 0.7180 (t) cc_final: 0.6843 (t) REVERT: A 715 ASP cc_start: 0.8204 (t0) cc_final: 0.7924 (t0) REVERT: A 924 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8580 (p90) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.0915 time to fit residues: 6.2732 Evaluate side-chains 46 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 924 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 68 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072112 restraints weight = 17492.934| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.16 r_work: 0.2735 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8411 Z= 0.107 Angle : 0.580 8.789 11564 Z= 0.273 Chirality : 0.050 0.475 1317 Planarity : 0.002 0.021 1290 Dihedral : 13.735 179.841 1562 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.77 % Allowed : 10.30 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 851 helix: 0.51 (0.23), residues: 532 sheet: -1.33 (0.93), residues: 34 loop : -0.80 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.009 0.001 TYR A 920 PHE 0.010 0.001 PHE A 916 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8411) covalent geometry : angle 0.58040 / 0.27 (11564) hydrogen bonds : bond 0.04005 / 2.05 ( 305) hydrogen bonds : angle 3.46011 / 1.37 ( 876) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.220 Fit side-chains REVERT: A 334 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8547 (tm-30) REVERT: A 470 ASP cc_start: 0.8068 (p0) cc_final: 0.7843 (t0) REVERT: A 685 CYS cc_start: 0.7172 (t) cc_final: 0.6848 (t) REVERT: A 715 ASP cc_start: 0.8178 (t0) cc_final: 0.7873 (t0) REVERT: A 924 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8442 (p90) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.0958 time to fit residues: 6.9431 Evaluate side-chains 42 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 924 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.089983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.072842 restraints weight = 17336.349| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.10 r_work: 0.2750 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8411 Z= 0.105 Angle : 0.573 8.574 11564 Z= 0.270 Chirality : 0.050 0.441 1317 Planarity : 0.002 0.021 1290 Dihedral : 13.696 179.784 1562 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.90 % Allowed : 11.07 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.29), residues: 851 helix: 0.73 (0.23), residues: 526 sheet: -1.26 (0.94), residues: 34 loop : -0.69 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.010 0.001 TYR A 920 PHE 0.010 0.001 PHE A 916 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 8411) covalent geometry : angle 0.57274 / 0.27 (11564) hydrogen bonds : bond 0.03871 / 1.99 ( 305) hydrogen bonds : angle 3.41381 / 1.35 ( 876) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.183 Fit side-chains REVERT: A 116 MET cc_start: 0.8656 (tpp) cc_final: 0.8451 (mmp) REVERT: A 334 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 470 ASP cc_start: 0.8118 (p0) cc_final: 0.7873 (t0) REVERT: A 685 CYS cc_start: 0.7152 (t) cc_final: 0.6822 (t) REVERT: A 715 ASP cc_start: 0.8218 (t0) cc_final: 0.7934 (t0) REVERT: A 730 GLU cc_start: 0.8238 (mp0) cc_final: 0.7986 (mp0) REVERT: A 924 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8357 (p90) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.0862 time to fit residues: 6.2593 Evaluate side-chains 47 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 924 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.0170 chunk 63 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.073627 restraints weight = 17320.995| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.10 r_work: 0.2764 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8411 Z= 0.100 Angle : 0.566 8.614 11564 Z= 0.266 Chirality : 0.049 0.409 1317 Planarity : 0.002 0.023 1290 Dihedral : 13.656 179.478 1562 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.03 % Allowed : 11.33 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 851 helix: 0.86 (0.23), residues: 526 sheet: -1.20 (0.94), residues: 34 loop : -0.68 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.009 0.001 TYR A 920 PHE 0.008 0.001 PHE A 875 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8411) covalent geometry : angle 0.56623 / 0.27 (11564) hydrogen bonds : bond 0.03691 / 1.90 ( 305) hydrogen bonds : angle 3.34142 / 1.31 ( 876) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.228 Fit side-chains REVERT: A 334 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 470 ASP cc_start: 0.8140 (p0) cc_final: 0.7901 (t0) REVERT: A 703 ASP cc_start: 0.8238 (p0) cc_final: 0.7962 (m-30) REVERT: A 715 ASP cc_start: 0.8220 (t0) cc_final: 0.7930 (t0) REVERT: A 924 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8327 (p90) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.0827 time to fit residues: 6.2012 Evaluate side-chains 45 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 924 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.090806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.073599 restraints weight = 17260.496| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.10 r_work: 0.2760 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8411 Z= 0.102 Angle : 0.567 8.701 11564 Z= 0.266 Chirality : 0.049 0.374 1317 Planarity : 0.002 0.022 1290 Dihedral : 13.624 179.341 1562 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.90 % Allowed : 11.45 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.29), residues: 851 helix: 0.92 (0.23), residues: 526 sheet: -1.15 (0.94), residues: 34 loop : -0.72 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.010 0.001 TYR A 920 PHE 0.010 0.001 PHE A 916 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 8411) covalent geometry : angle 0.56738 / 0.27 (11564) hydrogen bonds : bond 0.03664 / 1.88 ( 305) hydrogen bonds : angle 3.33534 / 1.31 ( 876) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1702 Ramachandran restraints generated. 851 Oldfield, 0 Emsley, 851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.285 Fit side-chains REVERT: A 334 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 470 ASP cc_start: 0.8133 (p0) cc_final: 0.7873 (t0) REVERT: A 703 ASP cc_start: 0.8237 (p0) cc_final: 0.7939 (m-30) REVERT: A 715 ASP cc_start: 0.8277 (t0) cc_final: 0.7984 (t0) REVERT: A 730 GLU cc_start: 0.8245 (mp0) cc_final: 0.7982 (mp0) REVERT: A 924 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8365 (p90) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.0849 time to fit residues: 5.7094 Evaluate side-chains 45 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 924 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 0.0060 chunk 77 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.088796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.071388 restraints weight = 17376.881| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.12 r_work: 0.2715 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8411 Z= 0.117 Angle : 0.583 8.739 11564 Z= 0.275 Chirality : 0.049 0.329 1317 Planarity : 0.002 0.021 1290 Dihedral : 13.607 179.637 1562 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.90 % Allowed : 11.45 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.29), residues: 851 helix: 0.83 (0.23), residues: 533 sheet: -0.97 (0.89), residues: 39 loop : -0.83 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 584 TYR 0.012 0.001 TYR A 920 PHE 0.014 0.001 PHE A 916 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8411) covalent geometry : angle 0.58271 / 0.27 (11564) hydrogen bonds : bond 0.03985 / 2.05 ( 305) hydrogen bonds : angle 3.43088 / 1.34 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1284.58 seconds wall clock time: 22 minutes 55.86 seconds (1375.86 seconds total)