Starting phenix.real_space_refine on Wed Aug 5 19:09:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh5_53155/08_2026/9qh5_53155_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh5_53155/08_2026/9qh5_53155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qh5_53155/08_2026/9qh5_53155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh5_53155/08_2026/9qh5_53155.map" model { file = "/net/cci-nas-00/data/ceres_data/9qh5_53155/08_2026/9qh5_53155_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh5_53155/08_2026/9qh5_53155_neut.cif" } resolution = 3.09 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 51 5.16 5 C 6892 2.51 5 N 1835 2.21 5 O 2061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10846 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2331 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 273} Chain: "B" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7834 Classifications: {'peptide': 988} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 935} Chain breaks: 1 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.03, per 1000 atoms: 0.19 Number of scatterers: 10846 At special positions: 0 Unit cell: (87.55, 100.3, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 7 15.00 O 2061 8.00 N 1835 7.00 C 6892 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 238.0 milliseconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 49.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 4524 through 4533 Processing helix chain 'A' and resid 4559 through 4566 Processing helix chain 'A' and resid 4572 through 4586 removed outlier: 3.784A pdb=" N VAL A4583 " --> pdb=" O ALA A4579 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A4584 " --> pdb=" O GLN A4580 " (cutoff:3.500A) Processing helix chain 'A' and resid 4676 through 4680 removed outlier: 4.046A pdb=" N LYS A4680 " --> pdb=" O PRO A4677 " (cutoff:3.500A) Processing helix chain 'A' and resid 4687 through 4699 Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 3.776A pdb=" N GLU A4708 " --> pdb=" O TYR A4705 " (cutoff:3.500A) Processing helix chain 'A' and resid 4711 through 4715 Processing helix chain 'A' and resid 4717 through 4739 Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4751 through 4762 removed outlier: 3.631A pdb=" N LYS A4762 " --> pdb=" O HIS A4758 " (cutoff:3.500A) Processing helix chain 'A' and resid 4762 through 4778 removed outlier: 3.601A pdb=" N GLN A4778 " --> pdb=" O ILE A4774 " (cutoff:3.500A) Processing helix chain 'A' and resid 4779 through 4781 No H-bonds generated for 'chain 'A' and resid 4779 through 4781' Processing helix chain 'A' and resid 4786 through 4810 removed outlier: 3.634A pdb=" N GLN A4803 " --> pdb=" O ARG A4799 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A4806 " --> pdb=" O ALA A4802 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 6.971A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.608A pdb=" N GLY B 102 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.610A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 4.380A pdb=" N PHE B 150 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.637A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.682A pdb=" N GLU B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.363A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.507A pdb=" N GLU B 435 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 451 through 460 removed outlier: 3.688A pdb=" N ASN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.690A pdb=" N GLU B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 508 removed outlier: 3.633A pdb=" N ASN B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.671A pdb=" N ILE B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.570A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 552 removed outlier: 4.566A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 552 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.578A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.630A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.504A pdb=" N LEU B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 770 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 788 Processing helix chain 'B' and resid 821 through 834 Processing helix chain 'B' and resid 838 through 842 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 915 removed outlier: 3.827A pdb=" N THR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 921 removed outlier: 3.655A pdb=" N TYR B 921 " --> pdb=" O PHE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.694A pdb=" N LEU B1005 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B1007 " --> pdb=" O ARG B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing helix chain 'E' and resid 22 through 35 removed outlier: 3.577A pdb=" N ILE E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.552A pdb=" N GLN E 41 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.735A pdb=" N TYR E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540 removed outlier: 3.632A pdb=" N ASP A4538 " --> pdb=" O VAL A4599 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A4601 " --> pdb=" O ASP A4538 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A4602 " --> pdb=" O ILE A4608 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A4608 " --> pdb=" O ASP A4602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 3.727A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.693A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 removed outlier: 5.924A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 496 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 945 Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.471A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.471A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 12 through 16 removed outlier: 4.259A pdb=" N SER E 65 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 0.86 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: 3523 1.34 - 1.46: 1581 1.46 - 1.57: 5902 1.57 - 1.69: 7 1.69 - 1.81: 75 Bond restraints: 11088 Sorted by residual: bond pdb=" CA SER E 20 " pdb=" CB SER E 20 " ideal model delta sigma weight residual 1.539 1.498 0.041 1.20e-02 6.94e+03 1.15e+01 bond pdb=" CZ ARG C 74 " pdb=" NH2 ARG C 74 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 5.95e+00 bond pdb=" N SER E 20 " pdb=" CA SER E 20 " ideal model delta sigma weight residual 1.460 1.488 -0.029 1.28e-02 6.10e+03 5.05e+00 bond pdb=" N GLU E 18 " pdb=" CA GLU E 18 " ideal model delta sigma weight residual 1.453 1.479 -0.026 1.18e-02 7.18e+03 4.91e+00 bond pdb=" N ASP E 21 " pdb=" CA ASP E 21 " ideal model delta sigma weight residual 1.454 1.482 -0.029 1.34e-02 5.57e+03 4.68e+00 ... (remaining 11083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 14762 1.43 - 2.86: 214 2.86 - 4.30: 47 4.30 - 5.73: 10 5.73 - 7.16: 2 Bond angle restraints: 15035 Sorted by residual: angle pdb=" N CYS A4666 " pdb=" CA CYS A4666 " pdb=" CB CYS A4666 " ideal model delta sigma weight residual 110.55 103.39 7.16 1.57e+00 4.06e-01 2.08e+01 angle pdb=" CA THR E 22 " pdb=" CB THR E 22 " pdb=" OG1 THR E 22 " ideal model delta sigma weight residual 109.60 103.45 6.15 1.50e+00 4.44e-01 1.68e+01 angle pdb=" CA PRO E 19 " pdb=" C PRO E 19 " pdb=" O PRO E 19 " ideal model delta sigma weight residual 121.95 117.30 4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" CA VAL E 17 " pdb=" C VAL E 17 " pdb=" O VAL E 17 " ideal model delta sigma weight residual 121.64 118.24 3.40 9.80e-01 1.04e+00 1.20e+01 angle pdb=" N PRO E 19 " pdb=" CA PRO E 19 " pdb=" C PRO E 19 " ideal model delta sigma weight residual 111.34 106.02 5.32 1.55e+00 4.16e-01 1.18e+01 ... (remaining 15030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 6369 17.25 - 34.50: 300 34.50 - 51.75: 62 51.75 - 69.00: 9 69.00 - 86.25: 5 Dihedral angle restraints: 6745 sinusoidal: 2776 harmonic: 3969 Sorted by residual: dihedral pdb=" N LEU E 15 " pdb=" CA LEU E 15 " pdb=" CB LEU E 15 " pdb=" CG LEU E 15 " ideal model delta sinusoidal sigma weight residual -60.00 -113.82 53.82 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" N MET A4560 " pdb=" CA MET A4560 " pdb=" CB MET A4560 " pdb=" CG MET A4560 " ideal model delta sinusoidal sigma weight residual -60.00 -113.75 53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA MET E 1 " pdb=" CB MET E 1 " pdb=" CG MET E 1 " pdb=" SD MET E 1 " ideal model delta sinusoidal sigma weight residual -180.00 -127.81 -52.19 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 6742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1177 0.036 - 0.073: 364 0.073 - 0.109: 115 0.109 - 0.145: 29 0.145 - 0.181: 2 Chirality restraints: 1687 Sorted by residual: chirality pdb=" CA VAL E 17 " pdb=" N VAL E 17 " pdb=" C VAL E 17 " pdb=" CB VAL E 17 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA GLU E 18 " pdb=" N GLU E 18 " pdb=" C GLU E 18 " pdb=" CB GLU E 18 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE B 891 " pdb=" N ILE B 891 " pdb=" C ILE B 891 " pdb=" CB ILE B 891 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1684 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A4656 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A4657 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A4657 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A4657 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A4676 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A4677 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A4677 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A4677 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 546 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 547 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 547 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 547 " -0.018 5.00e-02 4.00e+02 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1565 2.76 - 3.47: 14562 3.47 - 4.19: 23035 4.19 - 4.90: 43214 Nonbonded interactions: 82378 Sorted by model distance: nonbonded pdb=" OG SER B 625 " pdb=" C ALA C 76 " model vdw 1.329 3.270 nonbonded pdb=" SG CYS A4666 " pdb=" CB ALA C 76 " model vdw 1.816 3.820 nonbonded pdb=" CG GLU E 24 " pdb=" OD1 ASP E 52 " model vdw 2.089 3.440 nonbonded pdb=" O LEU B 568 " pdb=" CB ALA E 76 " model vdw 2.101 3.460 nonbonded pdb=" OG SER B 625 " pdb=" O ALA C 76 " model vdw 2.229 3.040 ... (remaining 82373 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.004 0.041 11089 Z= 0.178 Angle : 0.485 7.162 15035 Z= 0.274 Chirality : 0.041 0.181 1687 Planarity : 0.003 0.043 1928 Dihedral : 10.729 86.251 4167 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.00 % Allowed : 3.67 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 1.93 (0.24), residues: 1348 helix: 2.50 (0.23), residues: 538 sheet: 0.96 (0.36), residues: 215 loop : 0.35 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4799 TYR 0.014 0.001 TYR A4660 PHE 0.009 0.001 PHE A4628 TRP 0.011 0.001 TRP A4673 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (11088) covalent geometry : angle 0.48527 / 0.27 (15035) hydrogen bonds : bond 0.19104 / 12.81 ( 515) hydrogen bonds : angle 6.12007 / 4.21 ( 1416) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 4644 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8606 (t0) REVERT: A 4673 TRP cc_start: 0.7157 (p-90) cc_final: 0.5955 (p-90) REVERT: B 619 GLU cc_start: 0.9402 (mp0) cc_final: 0.8591 (tp30) REVERT: B 621 GLU cc_start: 0.9447 (mm-30) cc_final: 0.8758 (pp20) REVERT: E 22 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.5919 (t) REVERT: E 58 ASP cc_start: 0.8925 (m-30) cc_final: 0.8615 (m-30) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.0928 time to fit residues: 9.1915 Evaluate side-chains 61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4644 ASN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain E residue 22 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.1980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN B 505 ASN B 858 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.038602 restraints weight = 35729.843| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 4.44 r_work: 0.2429 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11089 Z= 0.148 Angle : 0.476 4.897 15035 Z= 0.251 Chirality : 0.041 0.139 1687 Planarity : 0.004 0.045 1928 Dihedral : 4.992 58.573 1508 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.00 % Allowed : 4.67 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 1.98 (0.24), residues: 1348 helix: 2.56 (0.23), residues: 545 sheet: 0.71 (0.36), residues: 212 loop : 0.44 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 54 TYR 0.014 0.001 TYR B 611 PHE 0.009 0.001 PHE B 971 TRP 0.005 0.001 TRP B 378 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11088) covalent geometry : angle 0.47581 / 0.25 (15035) hydrogen bonds : bond 0.04544 / 2.99 ( 515) hydrogen bonds : angle 4.74292 / 3.23 ( 1416) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.414 Fit side-chains REVERT: A 4644 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8594 (t0) REVERT: A 4673 TRP cc_start: 0.7023 (p-90) cc_final: 0.6378 (p-90) REVERT: B 162 MET cc_start: 0.9349 (mmm) cc_final: 0.9041 (mmm) REVERT: B 619 GLU cc_start: 0.9394 (mp0) cc_final: 0.8588 (tp30) REVERT: B 621 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8782 (pp20) REVERT: E 31 GLN cc_start: 0.9362 (tt0) cc_final: 0.9108 (tt0) REVERT: E 34 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8985 (mm-30) REVERT: E 58 ASP cc_start: 0.9012 (m-30) cc_final: 0.8762 (m-30) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0894 time to fit residues: 8.7899 Evaluate side-chains 59 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4644 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 855 HIS Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 104 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.039467 restraints weight = 35960.761| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 4.43 r_work: 0.2453 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11089 Z= 0.108 Angle : 0.430 4.720 15035 Z= 0.227 Chirality : 0.040 0.135 1687 Planarity : 0.003 0.045 1928 Dihedral : 4.754 56.234 1505 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.08 % Allowed : 5.34 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.09 (0.24), residues: 1348 helix: 2.64 (0.23), residues: 551 sheet: 0.81 (0.36), residues: 213 loop : 0.47 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.008 0.001 TYR B 611 PHE 0.009 0.001 PHE B 656 TRP 0.007 0.001 TRP B 378 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11088) covalent geometry : angle 0.43027 / 0.23 (15035) hydrogen bonds : bond 0.03729 / 2.44 ( 515) hydrogen bonds : angle 4.39902 / 2.98 ( 1416) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 4644 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8580 (t0) REVERT: B 162 MET cc_start: 0.9370 (mmm) cc_final: 0.9062 (mmm) REVERT: B 619 GLU cc_start: 0.9421 (mp0) cc_final: 0.8618 (tp30) REVERT: B 621 GLU cc_start: 0.9418 (mm-30) cc_final: 0.8781 (pp20) REVERT: E 31 GLN cc_start: 0.9370 (tt0) cc_final: 0.9125 (tt0) REVERT: E 34 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8997 (mm-30) REVERT: E 58 ASP cc_start: 0.9061 (m-30) cc_final: 0.8819 (m-30) outliers start: 13 outliers final: 9 residues processed: 65 average time/residue: 0.1016 time to fit residues: 9.7677 Evaluate side-chains 61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4644 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 855 HIS Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.039511 restraints weight = 35980.823| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 4.45 r_work: 0.2456 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11089 Z= 0.104 Angle : 0.428 10.085 15035 Z= 0.221 Chirality : 0.040 0.133 1687 Planarity : 0.003 0.045 1928 Dihedral : 4.620 53.509 1505 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.08 % Allowed : 6.17 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.10 (0.24), residues: 1348 helix: 2.67 (0.23), residues: 552 sheet: 0.79 (0.36), residues: 213 loop : 0.46 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.008 0.001 TYR B 611 PHE 0.008 0.001 PHE B 656 TRP 0.005 0.001 TRP A4673 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (11088) covalent geometry : angle 0.42809 / 0.22 (15035) hydrogen bonds : bond 0.03435 / 2.24 ( 515) hydrogen bonds : angle 4.24263 / 2.87 ( 1416) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.308 Fit side-chains REVERT: B 162 MET cc_start: 0.9385 (mmm) cc_final: 0.9061 (mmm) REVERT: B 619 GLU cc_start: 0.9433 (mp0) cc_final: 0.8641 (tp30) REVERT: B 621 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8791 (pp20) REVERT: B 677 HIS cc_start: 0.8406 (t-170) cc_final: 0.8189 (t-170) REVERT: E 31 GLN cc_start: 0.9395 (tt0) cc_final: 0.9159 (tt0) REVERT: E 58 ASP cc_start: 0.9071 (m-30) cc_final: 0.8825 (m-30) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.0845 time to fit residues: 7.9217 Evaluate side-chains 58 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 59 optimal weight: 0.2980 chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.039145 restraints weight = 35760.628| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.42 r_work: 0.2438 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11089 Z= 0.134 Angle : 0.441 7.856 15035 Z= 0.229 Chirality : 0.040 0.132 1687 Planarity : 0.003 0.046 1928 Dihedral : 4.567 50.047 1502 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.08 % Allowed : 6.51 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.13 (0.24), residues: 1348 helix: 2.72 (0.23), residues: 552 sheet: 0.74 (0.36), residues: 213 loop : 0.47 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.007 0.001 TYR B 611 PHE 0.009 0.001 PHE B 656 TRP 0.043 0.001 TRP A4673 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (11088) covalent geometry : angle 0.44145 / 0.23 (15035) hydrogen bonds : bond 0.03674 / 2.39 ( 515) hydrogen bonds : angle 4.24505 / 2.86 ( 1416) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.336 Fit side-chains REVERT: A 4674 HIS cc_start: 0.6920 (t70) cc_final: 0.6508 (t-170) REVERT: B 162 MET cc_start: 0.9403 (mmm) cc_final: 0.9077 (mmm) REVERT: B 619 GLU cc_start: 0.9420 (mp0) cc_final: 0.8644 (tp30) REVERT: B 621 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8778 (pp20) REVERT: B 677 HIS cc_start: 0.8400 (t-170) cc_final: 0.8170 (t-170) REVERT: B 841 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: E 31 GLN cc_start: 0.9389 (tt0) cc_final: 0.9149 (tt0) REVERT: E 58 ASP cc_start: 0.9057 (m-30) cc_final: 0.8805 (m-30) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.0881 time to fit residues: 8.3038 Evaluate side-chains 60 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 29 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4778 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.037396 restraints weight = 35728.238| |-----------------------------------------------------------------------------| r_work (start): 0.2532 rms_B_bonded: 4.30 r_work: 0.2344 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 11089 Z= 0.271 Angle : 0.552 6.827 15035 Z= 0.285 Chirality : 0.043 0.131 1687 Planarity : 0.004 0.048 1928 Dihedral : 4.850 45.500 1502 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 6.59 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 1.92 (0.24), residues: 1348 helix: 2.65 (0.23), residues: 549 sheet: 0.49 (0.35), residues: 216 loop : 0.32 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 642 TYR 0.009 0.001 TYR A4727 PHE 0.013 0.001 PHE A4628 TRP 0.026 0.001 TRP A4673 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.27 (11088) covalent geometry : angle 0.55165 / 0.28 (15035) hydrogen bonds : bond 0.05036 / 3.26 ( 515) hydrogen bonds : angle 4.57932 / 3.11 ( 1416) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.426 Fit side-chains REVERT: B 66 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8216 (tt) REVERT: B 619 GLU cc_start: 0.9396 (mp0) cc_final: 0.8610 (tp30) REVERT: B 621 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8803 (pp20) REVERT: B 841 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8565 (m-30) REVERT: E 58 ASP cc_start: 0.8939 (m-30) cc_final: 0.8686 (m-30) outliers start: 18 outliers final: 10 residues processed: 65 average time/residue: 0.0971 time to fit residues: 9.4615 Evaluate side-chains 58 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.057940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.039985 restraints weight = 35537.702| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 4.37 r_work: 0.2470 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11089 Z= 0.084 Angle : 0.434 7.367 15035 Z= 0.226 Chirality : 0.039 0.137 1687 Planarity : 0.003 0.048 1928 Dihedral : 4.539 47.328 1502 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.17 % Allowed : 6.92 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.08 (0.24), residues: 1348 helix: 2.67 (0.23), residues: 553 sheet: 0.71 (0.36), residues: 213 loop : 0.46 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.008 0.001 TYR B 979 PHE 0.009 0.001 PHE B 971 TRP 0.024 0.001 TRP A4673 HIS 0.002 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.08 (11088) covalent geometry : angle 0.43426 / 0.23 (15035) hydrogen bonds : bond 0.03035 / 2.00 ( 515) hydrogen bonds : angle 4.12245 / 2.77 ( 1416) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.375 Fit side-chains REVERT: A 4674 HIS cc_start: 0.6625 (t70) cc_final: 0.6306 (t-170) REVERT: B 66 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8317 (tt) REVERT: B 162 MET cc_start: 0.9404 (mmm) cc_final: 0.9136 (mmm) REVERT: B 619 GLU cc_start: 0.9392 (mp0) cc_final: 0.8642 (tp30) REVERT: B 621 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8752 (pp20) REVERT: B 841 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8598 (m-30) REVERT: E 58 ASP cc_start: 0.9062 (m-30) cc_final: 0.8809 (m-30) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.0981 time to fit residues: 9.2571 Evaluate side-chains 60 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 62 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.039080 restraints weight = 35707.834| |-----------------------------------------------------------------------------| r_work (start): 0.2573 rms_B_bonded: 4.40 r_work: 0.2383 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11089 Z= 0.133 Angle : 0.447 6.928 15035 Z= 0.232 Chirality : 0.040 0.132 1687 Planarity : 0.003 0.047 1928 Dihedral : 4.527 46.461 1502 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.25 % Allowed : 6.92 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.12 (0.24), residues: 1348 helix: 2.72 (0.23), residues: 553 sheet: 0.70 (0.36), residues: 213 loop : 0.46 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 54 TYR 0.008 0.001 TYR A4621 PHE 0.009 0.001 PHE B 971 TRP 0.019 0.001 TRP A4673 HIS 0.003 0.000 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (11088) covalent geometry : angle 0.44728 / 0.23 (15035) hydrogen bonds : bond 0.03557 / 2.31 ( 515) hydrogen bonds : angle 4.16784 / 2.81 ( 1416) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.393 Fit side-chains REVERT: B 66 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 162 MET cc_start: 0.9379 (mmm) cc_final: 0.9044 (mmm) REVERT: B 619 GLU cc_start: 0.9374 (mp0) cc_final: 0.8629 (tp30) REVERT: B 621 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8741 (pp20) REVERT: B 841 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8576 (m-30) REVERT: E 58 ASP cc_start: 0.9006 (m-30) cc_final: 0.8752 (m-30) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.0973 time to fit residues: 9.4076 Evaluate side-chains 61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 127 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.038857 restraints weight = 35569.281| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 4.39 r_work: 0.2436 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11089 Z= 0.142 Angle : 0.458 7.647 15035 Z= 0.238 Chirality : 0.040 0.141 1687 Planarity : 0.003 0.047 1928 Dihedral : 4.548 46.070 1502 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.33 % Allowed : 7.01 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.09 (0.24), residues: 1348 helix: 2.73 (0.23), residues: 551 sheet: 0.66 (0.36), residues: 213 loop : 0.44 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 642 TYR 0.007 0.001 TYR A4621 PHE 0.009 0.001 PHE B 971 TRP 0.018 0.001 TRP A4673 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (11088) covalent geometry : angle 0.45821 / 0.24 (15035) hydrogen bonds : bond 0.03719 / 2.41 ( 515) hydrogen bonds : angle 4.19411 / 2.83 ( 1416) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.360 Fit side-chains REVERT: B 66 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 162 MET cc_start: 0.9412 (mmm) cc_final: 0.9086 (mmm) REVERT: B 621 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8643 (pp20) REVERT: B 841 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8580 (m-30) REVERT: E 58 ASP cc_start: 0.9005 (m-30) cc_final: 0.8743 (m-30) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 0.0858 time to fit residues: 8.0619 Evaluate side-chains 60 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 791 LYS Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 66 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4674 HIS B 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.040950 restraints weight = 34713.114| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 4.32 r_work: 0.2483 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11089 Z= 0.082 Angle : 0.429 7.566 15035 Z= 0.222 Chirality : 0.039 0.160 1687 Planarity : 0.003 0.048 1928 Dihedral : 4.392 47.382 1502 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.92 % Allowed : 7.51 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.17 (0.24), residues: 1348 helix: 2.72 (0.23), residues: 555 sheet: 0.79 (0.36), residues: 213 loop : 0.51 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 54 TYR 0.007 0.001 TYR B 979 PHE 0.008 0.001 PHE B 656 TRP 0.020 0.001 TRP A4673 HIS 0.003 0.000 HIS A4674 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (11088) covalent geometry : angle 0.42932 / 0.22 (15035) hydrogen bonds : bond 0.02855 / 1.87 ( 515) hydrogen bonds : angle 4.00699 / 2.69 ( 1416) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.269 Fit side-chains REVERT: B 66 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8265 (tt) REVERT: B 162 MET cc_start: 0.9403 (mmm) cc_final: 0.9123 (mmm) REVERT: B 621 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8625 (pp20) REVERT: B 841 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8588 (m-30) REVERT: B 985 MET cc_start: 0.8309 (tmm) cc_final: 0.8089 (tmm) REVERT: E 58 ASP cc_start: 0.9054 (m-30) cc_final: 0.8799 (m-30) outliers start: 11 outliers final: 8 residues processed: 60 average time/residue: 0.0853 time to fit residues: 7.5719 Evaluate side-chains 58 residues out of total 1199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 449 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 841 ASP Chi-restraints excluded: chain B residue 936 THR Chi-restraints excluded: chain E residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.041850 restraints weight = 34980.051| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 4.36 r_work: 0.2475 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11089 Z= 0.092 Angle : 0.432 7.755 15035 Z= 0.224 Chirality : 0.039 0.153 1687 Planarity : 0.003 0.047 1928 Dihedral : 4.344 47.497 1501 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.83 % Allowed : 7.67 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % Cis-general : 0.08 % 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: 2.22 (0.24), residues: 1348 helix: 2.75 (0.23), residues: 555 sheet: 0.82 (0.36), residues: 213 loop : 0.54 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 54 TYR 0.007 0.001 TYR A4621 PHE 0.009 0.001 PHE B 656 TRP 0.017 0.001 TRP A4673 HIS 0.004 0.000 HIS A4674 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (11088) covalent geometry : angle 0.43228 / 0.22 (15035) hydrogen bonds : bond 0.02965 / 1.92 ( 515) hydrogen bonds : angle 3.99774 / 2.68 ( 1416) Misc. bond : bond 0.00034 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.97 seconds wall clock time: 34 minutes 36.60 seconds (2076.60 seconds total)