Starting phenix.real_space_refine on Wed Feb 4 10:06:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ogc_70461/02_2026/9ogc_70461_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ogc_70461/02_2026/9ogc_70461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ogc_70461/02_2026/9ogc_70461_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ogc_70461/02_2026/9ogc_70461_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ogc_70461/02_2026/9ogc_70461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ogc_70461/02_2026/9ogc_70461.map" } resolution = 3.37 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= 0.010 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 S 63 5.16 5 C 6236 2.51 5 N 1643 2.21 5 O 1813 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9758 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6419 Classifications: {'peptide': 792} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 762} Chain breaks: 3 Chain: "B" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1807 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain: "E" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain breaks: 1 Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 834 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'K85': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.17 Number of scatterers: 9758 At special positions: 0 Unit cell: (66.36, 110.88, 172.2, 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 63 16.00 F 3 9.00 O 1813 8.00 N 1643 7.00 C 6236 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: 0.67 Conformation dependent library (CDL) restraints added in 447.2 milliseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 2 sheets defined 75.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.509A pdb=" N ILE A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 312 through 340 removed outlier: 6.731A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.612A pdb=" N SER A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 382 Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 409 through 423 removed outlier: 4.203A pdb=" N PHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 468 Processing helix chain 'A' and resid 468 through 486 removed outlier: 3.750A pdb=" N THR A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 509 through 531 Processing helix chain 'A' and resid 533 through 550 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.551A pdb=" N LYS A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 601 removed outlier: 4.002A pdb=" N PHE A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 600 " --> pdb=" O ARG A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.587A pdb=" N GLU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 623 removed outlier: 3.789A pdb=" N CYS A 623 " --> pdb=" O ASN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 642 Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 658 through 675 Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 706 through 736 removed outlier: 5.412A pdb=" N LEU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 removed outlier: 3.616A pdb=" N THR A 740 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 766 Processing helix chain 'A' and resid 768 through 775 Processing helix chain 'A' and resid 776 through 791 removed outlier: 4.491A pdb=" N ILE A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 796 removed outlier: 3.747A pdb=" N ARG A 796 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 811 removed outlier: 4.386A pdb=" N LEU A 801 " --> pdb=" O GLU A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 removed outlier: 4.025A pdb=" N ALA A 817 " --> pdb=" O HIS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 826 through 836 removed outlier: 3.994A pdb=" N ASN A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS A 836 " --> pdb=" O ASN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.510A pdb=" N THR A 846 " --> pdb=" O PRO A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 4.124A pdb=" N PHE A 863 " --> pdb=" O CYS A 859 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 864 " --> pdb=" O PHE A 860 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 865 " --> pdb=" O PRO A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 882 removed outlier: 3.537A pdb=" N PHE A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 905 removed outlier: 3.735A pdb=" N ALA A 905 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 933 removed outlier: 3.764A pdb=" N GLN A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N CYS A 920 " --> pdb=" O GLN A 916 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 955 Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 990 through 1004 Processing helix chain 'A' and resid 1007 through 1027 Processing helix chain 'A' and resid 1030 through 1056 removed outlier: 3.797A pdb=" N PHE A1034 " --> pdb=" O THR A1030 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A1036 " --> pdb=" O ASP A1032 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A1055 " --> pdb=" O LYS A1051 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A1056 " --> pdb=" O ARG A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.785A pdb=" N LYS B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 removed outlier: 3.533A pdb=" N LYS B 96 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.539A pdb=" N TRP B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'B' and resid 186 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 246 removed outlier: 3.570A pdb=" N ALA B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'B' and resid 266 through 273 removed outlier: 3.736A pdb=" N GLY B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 96 through 110 removed outlier: 4.309A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 36 removed outlier: 3.822A pdb=" N LEU F 27 " --> pdb=" O THR F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.129A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU E 28 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE F 15 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E 30 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASP F 17 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR F 16 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 5 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N ALA F 73 " --> pdb=" O ASP F 2 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE F 4 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL F 75 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET F 6 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 77 " --> pdb=" O MET F 6 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG F 8 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE F 79 " --> pdb=" O ARG F 8 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 78 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG F 43 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.129A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU E 28 " --> pdb=" O THR F 13 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE F 15 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E 30 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ASP F 17 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR F 16 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 5 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N ALA F 73 " --> pdb=" O ASP F 2 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE F 4 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL F 75 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N MET F 6 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU F 77 " --> pdb=" O MET F 6 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG F 8 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE F 79 " --> pdb=" O ARG F 8 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1875 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: 1.42 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1746 1.32 - 1.44: 2406 1.44 - 1.57: 5700 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 9952 Sorted by residual: bond pdb=" C11 K85 A1101 " pdb=" O15 K85 A1101 " ideal model delta sigma weight residual 1.342 1.377 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" N4 K85 A1101 " pdb=" N5 K85 A1101 " ideal model delta sigma weight residual 1.331 1.360 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 K85 A1101 " pdb=" O1' K85 A1101 " ideal model delta sigma weight residual 1.322 1.342 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C17 K85 A1101 " pdb=" F18 K85 A1101 " ideal model delta sigma weight residual 1.342 1.327 0.015 2.00e-02 2.50e+03 5.65e-01 bond pdb=" CB GLU A 361 " pdb=" CG GLU A 361 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.37e-01 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 13121 1.16 - 2.32: 278 2.32 - 3.48: 54 3.48 - 4.64: 30 4.64 - 5.80: 7 Bond angle restraints: 13490 Sorted by residual: angle pdb=" N PHE A 927 " pdb=" CA PHE A 927 " pdb=" CB PHE A 927 " ideal model delta sigma weight residual 110.01 113.31 -3.30 1.45e+00 4.76e-01 5.18e+00 angle pdb=" C ILE A 926 " pdb=" N PHE A 927 " pdb=" CA PHE A 927 " ideal model delta sigma weight residual 120.44 117.59 2.85 1.30e+00 5.92e-01 4.79e+00 angle pdb=" N TYR B 266 " pdb=" CA TYR B 266 " pdb=" C TYR B 266 " ideal model delta sigma weight residual 110.80 106.36 4.44 2.13e+00 2.20e-01 4.34e+00 angle pdb=" CB MET A 804 " pdb=" CG MET A 804 " pdb=" SD MET A 804 " ideal model delta sigma weight residual 112.70 118.50 -5.80 3.00e+00 1.11e-01 3.74e+00 angle pdb=" N MET A 476 " pdb=" CA MET A 476 " pdb=" CB MET A 476 " ideal model delta sigma weight residual 110.12 112.74 -2.62 1.47e+00 4.63e-01 3.19e+00 ... (remaining 13485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5461 17.55 - 35.11: 482 35.11 - 52.66: 79 52.66 - 70.22: 19 70.22 - 87.77: 9 Dihedral angle restraints: 6050 sinusoidal: 2465 harmonic: 3585 Sorted by residual: dihedral pdb=" CA HIS A 884 " pdb=" C HIS A 884 " pdb=" N THR A 885 " pdb=" CA THR A 885 " ideal model delta harmonic sigma weight residual -180.00 -160.83 -19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA VAL A 784 " pdb=" C VAL A 784 " pdb=" N LEU A 785 " pdb=" CA LEU A 785 " ideal model delta harmonic sigma weight residual -180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB GLU A 575 " pdb=" CG GLU A 575 " pdb=" CD GLU A 575 " pdb=" OE1 GLU A 575 " ideal model delta sinusoidal sigma weight residual 0.00 87.77 -87.77 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1038 0.028 - 0.055: 343 0.055 - 0.083: 115 0.083 - 0.110: 37 0.110 - 0.138: 17 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA ILE E 90 " pdb=" N ILE E 90 " pdb=" C ILE E 90 " pdb=" CB ILE E 90 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA ILE A1065 " pdb=" N ILE A1065 " pdb=" C ILE A1065 " pdb=" CB ILE A1065 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL A 968 " pdb=" N VAL A 968 " pdb=" C VAL A 968 " pdb=" CB VAL A 968 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 1547 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 866 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 867 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 867 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 867 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 792 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO A 793 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 46 " -0.005 2.00e-02 2.50e+03 9.92e-03 9.84e-01 pdb=" C LYS F 46 " 0.017 2.00e-02 2.50e+03 pdb=" O LYS F 46 " -0.006 2.00e-02 2.50e+03 pdb=" N ASP F 47 " -0.006 2.00e-02 2.50e+03 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 139 2.61 - 3.18: 9672 3.18 - 3.75: 15720 3.75 - 4.33: 20808 4.33 - 4.90: 33909 Nonbonded interactions: 80248 Sorted by model distance: nonbonded pdb=" OG SER E 23 " pdb=" O ASP E 25 " model vdw 2.038 3.040 nonbonded pdb=" OG SER A 490 " pdb=" OD1 ASN A 493 " model vdw 2.080 3.040 nonbonded pdb=" O LYS F 19 " pdb=" OG SER F 22 " model vdw 2.094 3.040 nonbonded pdb=" O LEU A 298 " pdb=" OH TYR A 353 " model vdw 2.129 3.040 nonbonded pdb=" NH2 ARG F 80 " pdb=" OD1 ASP F 83 " model vdw 2.141 3.120 ... (remaining 80243 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: 2.730 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.050 Find NCS groups from input model: 0.040 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.003 0.035 9953 Z= 0.128 Angle : 0.483 5.802 13490 Z= 0.253 Chirality : 0.034 0.138 1550 Planarity : 0.003 0.034 1730 Dihedral : 13.901 87.771 3710 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 2.08 (0.24), residues: 1202 helix: 1.98 (0.18), residues: 831 sheet: 0.29 (1.16), residues: 19 loop : 0.05 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 458 TYR 0.008 0.001 TYR E 76 PHE 0.014 0.001 PHE A 927 TRP 0.007 0.001 TRP A 762 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9952) covalent geometry : angle 0.48337 (13490) hydrogen bonds : bond 0.16165 ( 627) hydrogen bonds : angle 5.56360 ( 1875) Misc. bond : bond 0.03089 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9420 (ppp) cc_final: 0.9088 (ppp) REVERT: A 298 LEU cc_start: 0.9326 (tp) cc_final: 0.9085 (tp) REVERT: A 338 GLU cc_start: 0.9046 (pt0) cc_final: 0.8702 (pt0) REVERT: A 348 MET cc_start: 0.8559 (mmp) cc_final: 0.8218 (mmm) REVERT: A 748 MET cc_start: 0.8360 (mtm) cc_final: 0.8086 (mtp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0641 time to fit residues: 7.6614 Evaluate side-chains 64 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.0870 chunk 117 optimal weight: 4.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.077943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057028 restraints weight = 50834.119| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 4.53 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9953 Z= 0.134 Angle : 0.584 11.047 13490 Z= 0.297 Chirality : 0.040 0.149 1550 Planarity : 0.004 0.043 1730 Dihedral : 4.594 64.219 1310 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.83 % Allowed : 5.19 % Favored : 93.98 % 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: 2.32 (0.24), residues: 1202 helix: 2.08 (0.18), residues: 849 sheet: -0.75 (1.62), residues: 10 loop : 0.33 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 458 TYR 0.018 0.001 TYR A 372 PHE 0.015 0.001 PHE A 329 TRP 0.018 0.001 TRP A 762 HIS 0.004 0.001 HIS A 577 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9952) covalent geometry : angle 0.58366 (13490) hydrogen bonds : bond 0.04398 ( 627) hydrogen bonds : angle 4.27688 ( 1875) Misc. bond : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9359 (ppp) cc_final: 0.9100 (ppp) REVERT: A 338 GLU cc_start: 0.8905 (pt0) cc_final: 0.8522 (pt0) REVERT: A 348 MET cc_start: 0.8475 (mmp) cc_final: 0.8178 (mmm) REVERT: A 927 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.9200 (m-80) REVERT: A 949 MET cc_start: 0.9645 (mtt) cc_final: 0.9435 (ptp) REVERT: A 1051 LYS cc_start: 0.8900 (tppt) cc_final: 0.8592 (ptpp) REVERT: B 107 TYR cc_start: 0.8209 (m-80) cc_final: 0.8000 (m-80) outliers start: 9 outliers final: 2 residues processed: 77 average time/residue: 0.0644 time to fit residues: 7.7961 Evaluate side-chains 68 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain E residue 18 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.076769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055791 restraints weight = 50936.978| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.57 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9953 Z= 0.150 Angle : 0.545 12.755 13490 Z= 0.276 Chirality : 0.039 0.135 1550 Planarity : 0.004 0.045 1730 Dihedral : 4.522 59.475 1310 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.56 % Allowed : 8.06 % Favored : 91.39 % 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: 2.32 (0.24), residues: 1202 helix: 2.09 (0.18), residues: 848 sheet: -0.97 (1.59), residues: 10 loop : 0.31 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 458 TYR 0.013 0.001 TYR A 372 PHE 0.014 0.001 PHE A 329 TRP 0.011 0.001 TRP A 762 HIS 0.006 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9952) covalent geometry : angle 0.54459 (13490) hydrogen bonds : bond 0.04213 ( 627) hydrogen bonds : angle 4.16780 ( 1875) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9367 (ppp) cc_final: 0.9130 (ppp) REVERT: A 338 GLU cc_start: 0.8988 (pt0) cc_final: 0.8713 (pt0) REVERT: A 348 MET cc_start: 0.8462 (mmp) cc_final: 0.8195 (mmm) REVERT: A 927 PHE cc_start: 0.9533 (OUTLIER) cc_final: 0.9294 (m-80) REVERT: A 949 MET cc_start: 0.9656 (mtt) cc_final: 0.9424 (ptp) REVERT: B 107 TYR cc_start: 0.8355 (m-80) cc_final: 0.8097 (m-80) outliers start: 6 outliers final: 2 residues processed: 74 average time/residue: 0.0711 time to fit residues: 8.0689 Evaluate side-chains 67 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN B 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.077488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.056840 restraints weight = 51301.713| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.56 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9953 Z= 0.114 Angle : 0.527 10.344 13490 Z= 0.265 Chirality : 0.038 0.175 1550 Planarity : 0.004 0.045 1730 Dihedral : 4.444 56.204 1310 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.11 % Allowed : 8.89 % Favored : 90.00 % 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: 2.42 (0.25), residues: 1202 helix: 2.16 (0.18), residues: 845 sheet: -1.09 (1.55), residues: 10 loop : 0.39 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.018 0.001 TYR A 372 PHE 0.012 0.001 PHE A 329 TRP 0.013 0.001 TRP A 762 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9952) covalent geometry : angle 0.52705 (13490) hydrogen bonds : bond 0.03682 ( 627) hydrogen bonds : angle 3.97634 ( 1875) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9425 (ppp) cc_final: 0.9147 (ppp) REVERT: A 338 GLU cc_start: 0.9036 (pt0) cc_final: 0.8712 (pt0) REVERT: A 348 MET cc_start: 0.8515 (mmp) cc_final: 0.8193 (mmm) REVERT: A 658 MET cc_start: 0.8621 (mmm) cc_final: 0.8202 (mmm) REVERT: A 927 PHE cc_start: 0.9614 (OUTLIER) cc_final: 0.9400 (m-80) REVERT: B 107 TYR cc_start: 0.8242 (m-80) cc_final: 0.7979 (m-80) REVERT: F 26 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (pm20) outliers start: 12 outliers final: 2 residues processed: 76 average time/residue: 0.0718 time to fit residues: 8.6582 Evaluate side-chains 69 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.0030 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.077290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.056368 restraints weight = 50521.863| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 4.52 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9953 Z= 0.125 Angle : 0.534 9.639 13490 Z= 0.268 Chirality : 0.038 0.171 1550 Planarity : 0.004 0.044 1730 Dihedral : 4.400 53.071 1310 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.02 % Allowed : 9.81 % Favored : 89.17 % 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: 2.41 (0.25), residues: 1202 helix: 2.16 (0.18), residues: 845 sheet: -0.96 (1.57), residues: 10 loop : 0.38 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.017 0.001 TYR A 372 PHE 0.012 0.001 PHE A 329 TRP 0.010 0.001 TRP A 762 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9952) covalent geometry : angle 0.53370 (13490) hydrogen bonds : bond 0.03652 ( 627) hydrogen bonds : angle 3.97461 ( 1875) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.283 Fit side-chains REVERT: A 297 MET cc_start: 0.9355 (ppp) cc_final: 0.9113 (ppp) REVERT: A 338 GLU cc_start: 0.9044 (pt0) cc_final: 0.8740 (pt0) REVERT: A 348 MET cc_start: 0.8403 (mmp) cc_final: 0.8129 (mmm) REVERT: A 658 MET cc_start: 0.8595 (mmm) cc_final: 0.8260 (mmm) REVERT: A 949 MET cc_start: 0.9658 (mtm) cc_final: 0.9400 (ptp) REVERT: A 1059 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5764 (mt) REVERT: B 107 TYR cc_start: 0.8333 (m-80) cc_final: 0.8066 (m-80) REVERT: F 26 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8466 (mp0) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.0677 time to fit residues: 8.1236 Evaluate side-chains 73 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 105 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.077100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.056135 restraints weight = 50975.307| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.57 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9953 Z= 0.133 Angle : 0.536 9.767 13490 Z= 0.268 Chirality : 0.038 0.172 1550 Planarity : 0.004 0.045 1730 Dihedral : 4.360 49.392 1310 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.02 % Allowed : 10.65 % Favored : 88.33 % 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: 2.41 (0.25), residues: 1202 helix: 2.16 (0.18), residues: 846 sheet: -1.01 (1.55), residues: 10 loop : 0.37 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.014 0.001 TYR A 372 PHE 0.011 0.001 PHE A 329 TRP 0.010 0.001 TRP A 762 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9952) covalent geometry : angle 0.53566 (13490) hydrogen bonds : bond 0.03643 ( 627) hydrogen bonds : angle 3.96719 ( 1875) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.331 Fit side-chains REVERT: A 297 MET cc_start: 0.9367 (ppp) cc_final: 0.9136 (ppp) REVERT: A 333 HIS cc_start: 0.9223 (m90) cc_final: 0.8923 (m90) REVERT: A 338 GLU cc_start: 0.9068 (pt0) cc_final: 0.8786 (pt0) REVERT: A 348 MET cc_start: 0.8408 (mmp) cc_final: 0.8129 (mmm) REVERT: A 949 MET cc_start: 0.9652 (mtm) cc_final: 0.9364 (ptp) REVERT: A 1059 ILE cc_start: 0.6083 (OUTLIER) cc_final: 0.5777 (mt) REVERT: B 107 TYR cc_start: 0.8320 (m-80) cc_final: 0.8069 (m-80) REVERT: F 26 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8462 (mp0) outliers start: 11 outliers final: 5 residues processed: 78 average time/residue: 0.0628 time to fit residues: 7.8909 Evaluate side-chains 74 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 0.0470 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 GLN A 916 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.077797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.056818 restraints weight = 50818.546| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.65 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9953 Z= 0.107 Angle : 0.547 16.438 13490 Z= 0.266 Chirality : 0.037 0.171 1550 Planarity : 0.003 0.044 1730 Dihedral : 4.293 46.608 1310 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.11 % Allowed : 10.83 % Favored : 88.06 % 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: 2.45 (0.25), residues: 1202 helix: 2.18 (0.18), residues: 846 sheet: -0.91 (1.56), residues: 10 loop : 0.40 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.019 0.001 TYR A 372 PHE 0.010 0.001 PHE A 329 TRP 0.013 0.001 TRP A 762 HIS 0.003 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9952) covalent geometry : angle 0.54673 (13490) hydrogen bonds : bond 0.03415 ( 627) hydrogen bonds : angle 3.85617 ( 1875) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9359 (ppp) cc_final: 0.9139 (ppp) REVERT: A 333 HIS cc_start: 0.9229 (m90) cc_final: 0.8937 (m90) REVERT: A 338 GLU cc_start: 0.9064 (pt0) cc_final: 0.8787 (pt0) REVERT: A 348 MET cc_start: 0.8371 (mmp) cc_final: 0.8047 (mmm) REVERT: A 412 MET cc_start: 0.8933 (mpp) cc_final: 0.8432 (mpp) REVERT: A 1059 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5737 (mt) REVERT: B 107 TYR cc_start: 0.8244 (m-80) cc_final: 0.8004 (m-80) REVERT: F 26 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8473 (mp0) outliers start: 12 outliers final: 3 residues processed: 78 average time/residue: 0.0652 time to fit residues: 8.1761 Evaluate side-chains 72 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 735 ASN A 916 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.083987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.062797 restraints weight = 50972.243| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 4.52 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9953 Z= 0.118 Angle : 0.551 13.128 13490 Z= 0.274 Chirality : 0.038 0.174 1550 Planarity : 0.004 0.044 1730 Dihedral : 4.269 44.522 1310 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.93 % Allowed : 11.48 % Favored : 87.59 % 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: 2.42 (0.25), residues: 1202 helix: 2.17 (0.18), residues: 846 sheet: -1.00 (1.51), residues: 10 loop : 0.37 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.011 0.001 TYR A 372 PHE 0.010 0.001 PHE A 329 TRP 0.011 0.001 TRP A 762 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9952) covalent geometry : angle 0.55100 (13490) hydrogen bonds : bond 0.03454 ( 627) hydrogen bonds : angle 3.88950 ( 1875) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9486 (ppp) cc_final: 0.9182 (ppp) REVERT: A 333 HIS cc_start: 0.9131 (m90) cc_final: 0.8806 (m90) REVERT: A 338 GLU cc_start: 0.9059 (pt0) cc_final: 0.8787 (pt0) REVERT: A 348 MET cc_start: 0.8654 (mmp) cc_final: 0.8235 (mmm) REVERT: A 412 MET cc_start: 0.8995 (mpp) cc_final: 0.8528 (mpp) REVERT: A 583 MET cc_start: 0.8548 (tpt) cc_final: 0.8265 (tpt) REVERT: B 62 MET cc_start: 0.3808 (mmm) cc_final: 0.3579 (mmm) REVERT: F 26 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8511 (mp0) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.0605 time to fit residues: 7.4990 Evaluate side-chains 76 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 101 optimal weight: 0.0060 chunk 8 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.084241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.063063 restraints weight = 50551.729| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.50 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9953 Z= 0.112 Angle : 0.556 12.587 13490 Z= 0.274 Chirality : 0.038 0.172 1550 Planarity : 0.004 0.045 1730 Dihedral : 4.268 43.404 1310 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.02 % Allowed : 11.76 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.25), residues: 1202 helix: 2.15 (0.18), residues: 846 sheet: -1.15 (1.43), residues: 10 loop : 0.37 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 556 TYR 0.024 0.001 TYR A 372 PHE 0.009 0.001 PHE A 329 TRP 0.012 0.001 TRP A 762 HIS 0.005 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9952) covalent geometry : angle 0.55603 (13490) hydrogen bonds : bond 0.03364 ( 627) hydrogen bonds : angle 3.85194 ( 1875) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9482 (ppp) cc_final: 0.9178 (ppp) REVERT: A 333 HIS cc_start: 0.9133 (m90) cc_final: 0.8821 (m90) REVERT: A 338 GLU cc_start: 0.9003 (pt0) cc_final: 0.8732 (pt0) REVERT: A 348 MET cc_start: 0.8643 (mmp) cc_final: 0.8225 (mmm) REVERT: A 412 MET cc_start: 0.8998 (mpp) cc_final: 0.8534 (mpp) REVERT: A 583 MET cc_start: 0.8496 (tpt) cc_final: 0.8225 (tpt) REVERT: A 1051 LYS cc_start: 0.8925 (tppt) cc_final: 0.8566 (ptpp) REVERT: B 62 MET cc_start: 0.3804 (mmm) cc_final: 0.3541 (mmm) REVERT: F 26 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8503 (mp0) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 0.0685 time to fit residues: 8.2305 Evaluate side-chains 77 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.077787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.057042 restraints weight = 50680.811| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.50 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9953 Z= 0.116 Angle : 0.571 12.111 13490 Z= 0.281 Chirality : 0.038 0.171 1550 Planarity : 0.004 0.045 1730 Dihedral : 4.257 42.107 1310 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.65 % Allowed : 12.22 % Favored : 87.13 % 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: 2.41 (0.25), residues: 1202 helix: 2.16 (0.18), residues: 847 sheet: -1.14 (1.42), residues: 10 loop : 0.37 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 556 TYR 0.012 0.001 TYR A 657 PHE 0.009 0.001 PHE A 329 TRP 0.011 0.001 TRP A 762 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9952) covalent geometry : angle 0.57116 (13490) hydrogen bonds : bond 0.03412 ( 627) hydrogen bonds : angle 3.87606 ( 1875) Misc. bond : bond 0.00019 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 297 MET cc_start: 0.9411 (ppp) cc_final: 0.9164 (ppp) REVERT: A 333 HIS cc_start: 0.9232 (m90) cc_final: 0.8953 (m90) REVERT: A 338 GLU cc_start: 0.8947 (pt0) cc_final: 0.8680 (pt0) REVERT: A 348 MET cc_start: 0.8414 (mmp) cc_final: 0.8092 (mmm) REVERT: A 412 MET cc_start: 0.9003 (mpp) cc_final: 0.8544 (mpp) REVERT: A 886 MET cc_start: 0.8064 (mtp) cc_final: 0.7745 (mtt) REVERT: A 1051 LYS cc_start: 0.8867 (tppt) cc_final: 0.8557 (ptpp) REVERT: B 62 MET cc_start: 0.3928 (mmm) cc_final: 0.3651 (mmm) REVERT: F 26 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8464 (mp0) REVERT: F 45 TYR cc_start: 0.8294 (m-10) cc_final: 0.8061 (m-10) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.0641 time to fit residues: 7.8047 Evaluate side-chains 77 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 1046 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 26 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 9 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 916 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.078075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057151 restraints weight = 50942.630| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.63 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9953 Z= 0.113 Angle : 0.576 11.922 13490 Z= 0.283 Chirality : 0.038 0.180 1550 Planarity : 0.004 0.045 1730 Dihedral : 4.218 43.741 1310 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.74 % Allowed : 12.41 % Favored : 86.85 % 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: 2.43 (0.25), residues: 1202 helix: 2.17 (0.18), residues: 846 sheet: -0.46 (1.15), residues: 19 loop : 0.39 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.012 0.001 TYR A 657 PHE 0.012 0.001 PHE A 287 TRP 0.012 0.001 TRP A 762 HIS 0.004 0.001 HIS A 598 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9952) covalent geometry : angle 0.57559 (13490) hydrogen bonds : bond 0.03327 ( 627) hydrogen bonds : angle 3.86190 ( 1875) Misc. bond : bond 0.00007 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.66 seconds wall clock time: 32 minutes 0.83 seconds (1920.83 seconds total)