Starting phenix.real_space_refine on Mon Nov 17 20:04:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e9e_9013/11_2025/6e9e_9013.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e9e_9013/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6e9e_9013/11_2025/6e9e_9013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e9e_9013/11_2025/6e9e_9013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e9e_9013/11_2025/6e9e_9013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e9e_9013/11_2025/6e9e_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-2.0-5881/lib/python3.9/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: {'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: 2.06, per 1000 atoms: 0.25 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: 0.75 Conformation dependent library (CDL) restraints added in 226.6 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: 1.05 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: 1.44 Time building geometry restraints manager: 0.97 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: 1.320 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.00581 ( 8411) covalent geometry : angle 0.73279 (11564) hydrogen bonds : bond 0.30175 ( 305) hydrogen bonds : angle 9.26567 ( 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 : 0.403 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: 0.1587 time to fit residues: 29.0539 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 : 0.298 ------------------------------------------------------------------------------- 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... 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 = 0.3299 r_free = 0.3299 target = 0.096750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080631 restraints weight = 17325.207| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.14 r_work: 0.2895 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2824 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= 0.124 Angle : 0.569 7.039 11564 Z= 0.303 Chirality : 0.039 0.152 1317 Planarity : 0.003 0.031 1290 Dihedral : 15.717 102.520 1714 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.39 % Allowed : 6.18 % Favored : 93.44 % 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: -2.87 (0.25), residues: 851 helix: -1.80 (0.20), residues: 518 sheet: -2.87 (0.85), residues: 24 loop : -1.68 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 138 TYR 0.014 0.001 TYR A 447 PHE 0.011 0.001 PHE A 916 TRP 0.012 0.002 TRP A 297 HIS 0.003 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8411) covalent geometry : angle 0.56870 (11564) hydrogen bonds : bond 0.06480 ( 305) hydrogen bonds : angle 4.57450 ( 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 75 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.374 Fit side-chains REVERT: A 156 MET cc_start: 0.8340 (mmm) cc_final: 0.8119 (mmt) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.1056 time to fit residues: 10.8191 Evaluate side-chains 43 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.0870 chunk 68 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 720 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.079187 restraints weight = 17320.662| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.15 r_work: 0.2864 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8411 Z= 0.094 Angle : 0.481 7.290 11564 Z= 0.254 Chirality : 0.037 0.181 1317 Planarity : 0.002 0.026 1290 Dihedral : 15.493 104.880 1712 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.64 % Allowed : 7.72 % Favored : 91.63 % 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: -1.49 (0.27), residues: 851 helix: -0.63 (0.22), residues: 519 sheet: -2.30 (0.79), residues: 32 loop : -1.21 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.011 0.001 TYR A 880 PHE 0.010 0.001 PHE A 555 TRP 0.010 0.002 TRP A 829 HIS 0.003 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 8411) covalent geometry : angle 0.48107 (11564) hydrogen bonds : bond 0.04550 ( 305) hydrogen bonds : angle 3.80924 ( 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 69 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 470 ASP cc_start: 0.8137 (p0) cc_final: 0.7865 (t0) outliers start: 5 outliers final: 1 residues processed: 68 average time/residue: 0.1218 time to fit residues: 10.6729 Evaluate side-chains 48 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 835 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3143 r_free = 0.3143 target = 0.087622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.070869 restraints weight = 17786.475| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.14 r_work: 0.2708 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8411 Z= 0.147 Angle : 0.528 9.059 11564 Z= 0.275 Chirality : 0.040 0.159 1317 Planarity : 0.003 0.028 1290 Dihedral : 15.462 107.744 1710 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.16 % Allowed : 8.11 % Favored : 90.73 % 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: -1.17 (0.28), residues: 851 helix: -0.32 (0.22), residues: 532 sheet: -1.88 (0.82), residues: 34 loop : -1.27 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 930 TYR 0.014 0.001 TYR A 920 PHE 0.021 0.002 PHE A 916 TRP 0.011 0.002 TRP A 829 HIS 0.003 0.001 HIS A 124 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8411) covalent geometry : angle 0.52786 (11564) hydrogen bonds : bond 0.05003 ( 305) hydrogen bonds : angle 3.89115 ( 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 55 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.218 Fit side-chains REVERT: A 334 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8130 (tm-30) REVERT: A 470 ASP cc_start: 0.8203 (p0) cc_final: 0.7828 (t0) REVERT: A 685 CYS cc_start: 0.7123 (t) cc_final: 0.6760 (t) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.0999 time to fit residues: 7.5450 Evaluate side-chains 48 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 482 ILE 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 59 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7064 ------------------------------------------------------------------------------- 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 = 0.3131 r_free = 0.3131 target = 0.086677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.069847 restraints weight = 17655.692| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.13 r_work: 0.2687 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8411 Z= 0.137 Angle : 0.487 7.263 11564 Z= 0.257 Chirality : 0.039 0.161 1317 Planarity : 0.003 0.020 1290 Dihedral : 15.469 112.827 1710 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.29 % Allowed : 8.88 % Favored : 89.83 % 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: -0.73 (0.28), residues: 851 helix: 0.01 (0.22), residues: 533 sheet: -1.78 (0.87), residues: 34 loop : -1.05 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 covalent geometry : bond 0.00314 ( 8411) covalent geometry : angle 0.48736 (11564) hydrogen bonds : bond 0.04569 ( 305) hydrogen bonds : angle 3.75986 ( 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: 10 poor density : 44 time to evaluate : 0.216 Fit side-chains REVERT: A 156 MET cc_start: 0.8598 (mmm) cc_final: 0.8215 (mmt) REVERT: A 334 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 410 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8214 (mpt) REVERT: A 470 ASP cc_start: 0.8216 (p0) cc_final: 0.7861 (t0) REVERT: A 685 CYS cc_start: 0.7193 (t) cc_final: 0.6851 (t) REVERT: A 715 ASP cc_start: 0.8268 (t0) cc_final: 0.8007 (t0) REVERT: A 924 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8582 (p90) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 0.0975 time to fit residues: 7.3613 Evaluate side-chains 43 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 410 MET Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 909 HIS 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 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.086765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.069883 restraints weight = 17489.044| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.14 r_work: 0.2688 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.4723 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= 0.109 Angle : 0.464 8.414 11564 Z= 0.242 Chirality : 0.037 0.155 1317 Planarity : 0.002 0.020 1290 Dihedral : 15.440 113.112 1710 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.16 % Allowed : 9.78 % Favored : 89.06 % 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: -0.38 (0.28), residues: 851 helix: 0.30 (0.23), residues: 533 sheet: -1.46 (0.90), residues: 34 loop : -0.96 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 930 TYR 0.010 0.001 TYR A 920 PHE 0.014 0.001 PHE A 916 TRP 0.010 0.001 TRP A 829 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8411) covalent geometry : angle 0.46366 (11564) hydrogen bonds : bond 0.04249 ( 305) hydrogen bonds : angle 3.60921 ( 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 60 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.302 Fit side-chains REVERT: A 334 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 410 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7843 (mpt) REVERT: A 470 ASP cc_start: 0.8092 (p0) cc_final: 0.7798 (t0) REVERT: A 685 CYS cc_start: 0.7188 (t) cc_final: 0.6850 (t) REVERT: A 715 ASP cc_start: 0.8221 (t0) cc_final: 0.7948 (t0) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 0.1017 time to fit residues: 8.1833 Evaluate side-chains 46 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 835 ASP 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 68 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.086777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.069975 restraints weight = 17668.106| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.14 r_work: 0.2690 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8411 Z= 0.106 Angle : 0.466 8.490 11564 Z= 0.242 Chirality : 0.037 0.155 1317 Planarity : 0.002 0.020 1290 Dihedral : 15.424 113.594 1710 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.29 % Allowed : 10.68 % 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: 0.46 (0.23), residues: 533 sheet: -1.29 (0.93), residues: 34 loop : -0.92 (0.35), residues: 284 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 0.015 0.001 PHE A 578 TRP 0.010 0.001 TRP A 829 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8411) covalent geometry : angle 0.46569 (11564) hydrogen bonds : bond 0.04062 ( 305) hydrogen bonds : angle 3.53589 ( 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 55 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.324 Fit side-chains REVERT: A 334 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 410 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7841 (mpt) REVERT: A 470 ASP cc_start: 0.8069 (p0) cc_final: 0.7823 (t0) REVERT: A 685 CYS cc_start: 0.7145 (t) cc_final: 0.6814 (t) REVERT: A 715 ASP cc_start: 0.8255 (t0) cc_final: 0.7982 (t0) REVERT: A 924 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8336 (p90) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 0.0952 time to fit residues: 7.3298 Evaluate side-chains 47 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 410 MET 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: 5.9990 chunk 40 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.087675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.070741 restraints weight = 17619.318| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.15 r_work: 0.2707 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4956 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= 0.103 Angle : 0.460 8.243 11564 Z= 0.239 Chirality : 0.037 0.153 1317 Planarity : 0.002 0.020 1290 Dihedral : 15.393 113.989 1710 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.29 % Allowed : 11.33 % Favored : 87.39 % 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: -0.00 (0.29), residues: 851 helix: 0.60 (0.23), residues: 532 sheet: -1.22 (0.95), residues: 34 loop : -0.83 (0.36), residues: 285 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 0.016 0.001 PHE A 578 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 879 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8411) covalent geometry : angle 0.45973 (11564) hydrogen bonds : bond 0.03908 ( 305) hydrogen bonds : angle 3.51451 ( 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 52 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.316 Fit side-chains REVERT: A 334 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8614 (tm-30) REVERT: A 410 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7823 (mpt) REVERT: A 470 ASP cc_start: 0.8119 (p0) cc_final: 0.7850 (t0) REVERT: A 685 CYS cc_start: 0.7121 (t) cc_final: 0.6782 (t) REVERT: A 715 ASP cc_start: 0.8312 (t0) cc_final: 0.8045 (t0) REVERT: A 924 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8393 (p90) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.1022 time to fit residues: 7.4219 Evaluate side-chains 49 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 410 MET 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: 0.8980 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.0770 chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.089272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.072308 restraints weight = 17612.197| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.15 r_work: 0.2740 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.5092 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= 0.087 Angle : 0.439 8.053 11564 Z= 0.227 Chirality : 0.036 0.153 1317 Planarity : 0.002 0.021 1290 Dihedral : 15.364 114.339 1710 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.90 % Allowed : 11.58 % Favored : 87.52 % 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: 0.75 (0.23), residues: 532 sheet: -1.15 (0.97), residues: 34 loop : -0.77 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 930 TYR 0.008 0.001 TYR A 920 PHE 0.016 0.001 PHE A 578 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 8411) covalent geometry : angle 0.43859 (11564) hydrogen bonds : bond 0.03491 ( 305) hydrogen bonds : angle 3.39065 ( 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 60 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.187 Fit side-chains REVERT: A 334 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8312 (tm-30) REVERT: A 470 ASP cc_start: 0.8093 (p0) cc_final: 0.7873 (t0) REVERT: A 685 CYS cc_start: 0.7087 (t) cc_final: 0.6749 (t) REVERT: A 715 ASP cc_start: 0.8264 (t0) cc_final: 0.7982 (t0) REVERT: A 905 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8656 (mmtm) REVERT: A 924 PHE cc_start: 0.9126 (OUTLIER) cc_final: 0.8310 (p90) outliers start: 7 outliers final: 3 residues processed: 60 average time/residue: 0.0906 time to fit residues: 7.5776 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 : 0.313 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 25 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 = 0.3173 r_free = 0.3173 target = 0.089311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.072299 restraints weight = 17525.895| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.14 r_work: 0.2742 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 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 0.036 8411 Z= 0.090 Angle : 0.447 8.325 11564 Z= 0.231 Chirality : 0.036 0.153 1317 Planarity : 0.002 0.021 1290 Dihedral : 15.342 114.029 1710 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.64 % Allowed : 11.97 % Favored : 87.39 % 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: 0.82 (0.23), residues: 532 sheet: -1.18 (0.96), residues: 34 loop : -0.78 (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 0.009 0.001 PHE A 513 TRP 0.008 0.001 TRP A 829 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 8411) covalent geometry : angle 0.44733 (11564) hydrogen bonds : bond 0.03499 ( 305) hydrogen bonds : angle 3.31981 ( 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 49 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.335 Fit side-chains REVERT: A 334 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8405 (tm-30) REVERT: A 470 ASP cc_start: 0.8049 (p0) cc_final: 0.7817 (t0) REVERT: A 685 CYS cc_start: 0.7012 (t) cc_final: 0.6686 (t) REVERT: A 703 ASP cc_start: 0.8251 (p0) cc_final: 0.7996 (m-30) REVERT: A 715 ASP cc_start: 0.8269 (t0) cc_final: 0.7968 (t0) REVERT: A 905 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8628 (mmtm) REVERT: A 924 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8282 (p90) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.1060 time to fit residues: 7.1930 Evaluate side-chains 48 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 10 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.090043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.073600 restraints weight = 17533.239| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.08 r_work: 0.2755 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.5241 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= 0.088 Angle : 0.441 8.245 11564 Z= 0.227 Chirality : 0.036 0.156 1317 Planarity : 0.002 0.021 1290 Dihedral : 15.321 114.330 1710 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.77 % Allowed : 11.84 % Favored : 87.39 % 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: 0.34 (0.29), residues: 851 helix: 0.90 (0.23), residues: 532 sheet: -1.15 (0.96), residues: 34 loop : -0.78 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 584 TYR 0.010 0.001 TYR A 920 PHE 0.008 0.001 PHE A 875 TRP 0.008 0.001 TRP A 829 HIS 0.004 0.001 HIS A 767 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 8411) covalent geometry : angle 0.44131 (11564) hydrogen bonds : bond 0.03371 ( 305) hydrogen bonds : angle 3.26519 ( 876) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.39 seconds wall clock time: 26 minutes 57.96 seconds (1617.96 seconds total)