Starting phenix.real_space_refine on Tue Apr 29 02:02:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e9e_9013/04_2025/6e9e_9013.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9e_9013/04_2025/6e9e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6e9e_9013/04_2025/6e9e_9013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9e_9013/04_2025/6e9e_9013.map" model { file = "/net/cci-nas-00/data/ceres_data/6e9e_9013/04_2025/6e9e_9013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9e_9013/04_2025/6e9e_9013.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'RNA': 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: 5.57, per 1000 atoms: 0.68 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: 2.26 Conformation dependent library (CDL) restraints added in 840.4 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: 2.75 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: 2.59 Time building geometry restraints manager: 2.67 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: 11079 1.61 - 3.23: 426 3.23 - 4.84: 43 4.84 - 6.45: 12 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 - 20.81: 4885 20.81 - 41.61: 166 41.61 - 62.42: 62 62.42 - 83.22: 36 83.22 - 104.03: 2 Dihedral angle restraints: 5151 sinusoidal: 2586 harmonic: 2565 Sorted by residual: dihedral pdb=" CA ASN A 651 " pdb=" C ASN A 651 " pdb=" N PRO A 652 " pdb=" CA PRO A 652 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" O4' A B 13 " pdb=" C1' A B 13 " pdb=" N9 A B 13 " pdb=" C4 A B 13 " ideal model delta sinusoidal sigma weight residual 68.00 122.69 -54.69 1 1.70e+01 3.46e-03 1.40e+01 dihedral pdb=" CA GLN A 92 " pdb=" C GLN A 92 " pdb=" N LYS A 93 " pdb=" CA LYS A 93 " ideal model delta harmonic sigma weight residual 180.00 161.86 18.14 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 966 0.043 - 0.086: 285 0.086 - 0.130: 57 0.130 - 0.173: 6 0.173 - 0.216: 3 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA LYS A 189 " pdb=" N LYS A 189 " pdb=" C LYS A 189 " pdb=" CB LYS A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LEU A 191 " pdb=" N LEU A 191 " pdb=" C LEU A 191 " pdb=" CB LEU A 191 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CB ILE A 190 " pdb=" CA ILE A 190 " pdb=" CG1 ILE A 190 " pdb=" CG2 ILE A 190 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.43e-01 ... (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: 1.230 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.100 Process input model: 24.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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= 0.257 Angle : 0.733 8.068 11564 Z= 0.426 Chirality : 0.042 0.216 1317 Planarity : 0.003 0.046 1290 Dihedral : 13.742 104.026 3491 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.003 TRP A 455 HIS 0.005 0.002 HIS A 99 PHE 0.031 0.002 PHE A 916 TYR 0.022 0.002 TYR A 912 ARG 0.008 0.001 ARG A 666 Details of bonding type rmsd hydrogen bonds : bond 0.30175 ( 305) hydrogen bonds : angle 9.26567 ( 876) covalent geometry : bond 0.00581 ( 8411) covalent geometry : angle 0.73279 (11564) *********************** 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 : 0.946 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: 0.3376 time to fit residues: 62.1440 Evaluate side-chains 54 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 76 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3268 r_free = 0.3268 target = 0.094884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.078722 restraints weight = 17005.875| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.11 r_work: 0.2862 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8411 Z= 0.131 Angle : 0.580 7.040 11564 Z= 0.308 Chirality : 0.040 0.153 1317 Planarity : 0.004 0.031 1290 Dihedral : 15.704 103.056 1714 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.25), residues: 851 helix: -1.81 (0.20), residues: 518 sheet: -2.86 (0.85), residues: 24 loop : -1.68 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 297 HIS 0.003 0.001 HIS A 879 PHE 0.014 0.001 PHE A 916 TYR 0.014 0.001 TYR A 880 ARG 0.005 0.001 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.06492 ( 305) hydrogen bonds : angle 4.57506 ( 876) covalent geometry : bond 0.00277 ( 8411) covalent geometry : angle 0.58015 (11564) *********************** 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 73 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.936 Fit side-chains REVERT: A 156 MET cc_start: 0.8426 (mmm) cc_final: 0.8217 (mmt) REVERT: A 334 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7378 (tm-30) outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.2440 time to fit residues: 23.9806 Evaluate side-chains 39 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.093495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.076823 restraints weight = 17518.416| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.18 r_work: 0.2821 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8411 Z= 0.100 Angle : 0.485 7.289 11564 Z= 0.255 Chirality : 0.037 0.155 1317 Planarity : 0.002 0.024 1290 Dihedral : 15.486 106.613 1712 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.90 % Allowed : 7.21 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.27), residues: 851 helix: -0.62 (0.22), residues: 520 sheet: -2.36 (0.77), residues: 32 loop : -1.21 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 829 HIS 0.003 0.001 HIS A 879 PHE 0.010 0.001 PHE A 916 TYR 0.011 0.001 TYR A 880 ARG 0.004 0.000 ARG A 138 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 305) hydrogen bonds : angle 3.84789 ( 876) covalent geometry : bond 0.00210 ( 8411) covalent geometry : angle 0.48472 (11564) *********************** 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 65 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8481 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 470 ASP cc_start: 0.8166 (p0) cc_final: 0.7770 (t0) outliers start: 7 outliers final: 2 residues processed: 63 average time/residue: 0.2820 time to fit residues: 23.7332 Evaluate side-chains 47 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 10 optimal weight: 4.9990 chunk 81 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072271 restraints weight = 17503.718| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.16 r_work: 0.2733 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8411 Z= 0.116 Angle : 0.496 9.423 11564 Z= 0.258 Chirality : 0.038 0.160 1317 Planarity : 0.002 0.022 1290 Dihedral : 15.430 108.258 1710 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.77 % Allowed : 8.24 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.28), residues: 851 helix: -0.16 (0.22), residues: 527 sheet: -2.06 (0.81), residues: 34 loop : -1.22 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 829 HIS 0.003 0.001 HIS A 767 PHE 0.016 0.001 PHE A 916 TYR 0.012 0.001 TYR A 920 ARG 0.004 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 305) hydrogen bonds : angle 3.72733 ( 876) covalent geometry : bond 0.00258 ( 8411) covalent geometry : angle 0.49613 (11564) *********************** 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 52 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8102 (tm-30) REVERT: A 470 ASP cc_start: 0.8165 (p0) cc_final: 0.7792 (t0) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.2380 time to fit residues: 17.4171 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ASP 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 74 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 53 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.072826 restraints weight = 17358.689| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.16 r_work: 0.2748 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8411 Z= 0.094 Angle : 0.450 7.265 11564 Z= 0.234 Chirality : 0.037 0.155 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.410 110.452 1710 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.03 % Allowed : 8.37 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.28), residues: 851 helix: 0.28 (0.23), residues: 529 sheet: -1.59 (0.87), residues: 32 loop : -1.00 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 829 HIS 0.003 0.001 HIS A 879 PHE 0.010 0.001 PHE A 916 TYR 0.009 0.001 TYR A 920 ARG 0.003 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 305) hydrogen bonds : angle 3.51638 ( 876) covalent geometry : bond 0.00204 ( 8411) covalent geometry : angle 0.44954 (11564) *********************** 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 56 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.841 Fit side-chains REVERT: A 334 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8110 (tm-30) REVERT: A 470 ASP cc_start: 0.8124 (p0) cc_final: 0.7843 (t0) REVERT: A 715 ASP cc_start: 0.8018 (t0) cc_final: 0.7749 (t0) REVERT: A 924 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8478 (p90) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 0.2172 time to fit residues: 17.1762 Evaluate side-chains 40 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 924 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 3 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.089897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.073000 restraints weight = 17294.604| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.15 r_work: 0.2752 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8411 Z= 0.093 Angle : 0.454 7.321 11564 Z= 0.236 Chirality : 0.036 0.152 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.371 110.193 1710 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.64 % Allowed : 9.65 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 851 helix: 0.53 (0.23), residues: 528 sheet: -1.49 (0.89), residues: 34 loop : -0.92 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 829 HIS 0.003 0.001 HIS A 767 PHE 0.010 0.001 PHE A 916 TYR 0.009 0.001 TYR A 920 ARG 0.003 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 305) hydrogen bonds : angle 3.36991 ( 876) covalent geometry : bond 0.00200 ( 8411) covalent geometry : angle 0.45387 (11564) *********************** 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 50 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 470 ASP cc_start: 0.8102 (p0) cc_final: 0.7814 (t0) REVERT: A 703 ASP cc_start: 0.8247 (p0) cc_final: 0.7921 (m-30) REVERT: A 715 ASP cc_start: 0.8054 (t0) cc_final: 0.7749 (t0) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.2230 time to fit residues: 15.9707 Evaluate side-chains 42 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 872 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.072927 restraints weight = 17300.316| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.15 r_work: 0.2751 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8411 Z= 0.089 Angle : 0.439 7.316 11564 Z= 0.228 Chirality : 0.036 0.154 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.360 110.984 1710 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.90 % Allowed : 9.40 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.29), residues: 851 helix: 0.68 (0.23), residues: 533 sheet: -1.39 (0.91), residues: 34 loop : -0.81 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.003 0.001 HIS A 879 PHE 0.010 0.001 PHE A 916 TYR 0.009 0.001 TYR A 920 ARG 0.002 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 305) hydrogen bonds : angle 3.31851 ( 876) covalent geometry : bond 0.00193 ( 8411) covalent geometry : angle 0.43937 (11564) *********************** 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 52 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.8684 (tpp) cc_final: 0.8482 (mmp) REVERT: A 334 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 470 ASP cc_start: 0.8088 (p0) cc_final: 0.7845 (t0) REVERT: A 703 ASP cc_start: 0.8283 (p0) cc_final: 0.7853 (m-30) REVERT: A 715 ASP cc_start: 0.8084 (t0) cc_final: 0.7790 (t0) REVERT: A 924 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8460 (p90) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.2092 time to fit residues: 15.7434 Evaluate side-chains 46 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 872 GLU 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 54 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.089542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.072585 restraints weight = 17463.938| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.16 r_work: 0.2742 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8411 Z= 0.091 Angle : 0.439 7.316 11564 Z= 0.228 Chirality : 0.036 0.152 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.350 111.596 1710 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.64 % Allowed : 9.78 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.29), residues: 851 helix: 0.78 (0.23), residues: 533 sheet: -1.25 (0.93), residues: 34 loop : -0.83 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 PHE 0.015 0.001 PHE A 513 TYR 0.010 0.001 TYR A 920 ARG 0.003 0.000 ARG A 584 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 305) hydrogen bonds : angle 3.34410 ( 876) covalent geometry : bond 0.00198 ( 8411) covalent geometry : angle 0.43903 (11564) *********************** 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 49 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.8663 (tpp) cc_final: 0.8461 (mmp) REVERT: A 334 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 470 ASP cc_start: 0.8081 (p0) cc_final: 0.7825 (t0) REVERT: A 703 ASP cc_start: 0.8296 (p0) cc_final: 0.7901 (m-30) REVERT: A 715 ASP cc_start: 0.8172 (t0) cc_final: 0.7877 (t0) REVERT: A 806 ILE cc_start: 0.8797 (tp) cc_final: 0.8596 (tt) REVERT: A 924 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8422 (p90) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.2995 time to fit residues: 21.5577 Evaluate side-chains 45 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 872 GLU 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 6 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 63 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.0000 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.074700 restraints weight = 17659.321| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.18 r_work: 0.2782 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8411 Z= 0.080 Angle : 0.425 7.317 11564 Z= 0.220 Chirality : 0.035 0.152 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.339 112.124 1710 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.64 % Allowed : 10.04 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.29), residues: 851 helix: 0.91 (0.23), residues: 533 sheet: -1.16 (0.94), residues: 34 loop : -0.76 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.003 0.001 HIS A 767 PHE 0.008 0.001 PHE A 875 TYR 0.008 0.001 TYR A 920 ARG 0.003 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 305) hydrogen bonds : angle 3.24085 ( 876) covalent geometry : bond 0.00165 ( 8411) covalent geometry : angle 0.42477 (11564) *********************** 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 61 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 470 ASP cc_start: 0.8048 (p0) cc_final: 0.7809 (t0) REVERT: A 703 ASP cc_start: 0.8284 (p0) cc_final: 0.7981 (m-30) REVERT: A 715 ASP cc_start: 0.8104 (t0) cc_final: 0.7743 (t0) REVERT: A 806 ILE cc_start: 0.8767 (tp) cc_final: 0.8562 (tt) REVERT: A 924 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8408 (p90) outliers start: 5 outliers final: 1 residues processed: 61 average time/residue: 0.2178 time to fit residues: 19.0022 Evaluate side-chains 44 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 872 GLU 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 7 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN A 860 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.072906 restraints weight = 17322.377| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.14 r_work: 0.2753 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8411 Z= 0.096 Angle : 0.458 8.127 11564 Z= 0.235 Chirality : 0.036 0.153 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.322 111.989 1710 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.64 % Allowed : 10.81 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.29), residues: 851 helix: 0.94 (0.23), residues: 533 sheet: -1.10 (0.94), residues: 34 loop : -0.83 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.003 0.001 HIS A 767 PHE 0.017 0.001 PHE A 513 TYR 0.011 0.001 TYR A 920 ARG 0.003 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 305) hydrogen bonds : angle 3.30475 ( 876) covalent geometry : bond 0.00215 ( 8411) covalent geometry : angle 0.45775 (11564) ********************** 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 45 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.865 Fit side-chains REVERT: A 334 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8357 (tm-30) REVERT: A 470 ASP cc_start: 0.8043 (p0) cc_final: 0.7742 (t0) REVERT: A 703 ASP cc_start: 0.8284 (p0) cc_final: 0.7972 (m-30) REVERT: A 715 ASP cc_start: 0.8195 (t0) cc_final: 0.7874 (t0) REVERT: A 806 ILE cc_start: 0.8693 (tp) cc_final: 0.8481 (tt) REVERT: A 924 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8330 (p90) outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.2180 time to fit residues: 14.2201 Evaluate side-chains 42 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 872 GLU 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 44 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.089357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.072327 restraints weight = 17626.015| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.17 r_work: 0.2728 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8411 Z= 0.100 Angle : 0.463 8.377 11564 Z= 0.236 Chirality : 0.037 0.154 1317 Planarity : 0.002 0.019 1290 Dihedral : 15.321 113.222 1710 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.51 % Allowed : 10.94 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 851 helix: 0.96 (0.23), residues: 533 sheet: -1.07 (0.95), residues: 34 loop : -0.85 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 PHE 0.012 0.001 PHE A 916 TYR 0.011 0.001 TYR A 920 ARG 0.003 0.000 ARG A 930 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 305) hydrogen bonds : angle 3.32338 ( 876) covalent geometry : bond 0.00225 ( 8411) covalent geometry : angle 0.46261 (11564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3181.84 seconds wall clock time: 56 minutes 33.49 seconds (3393.49 seconds total)