Starting phenix.real_space_refine on Fri Jul 3 00:43:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh6_40033/07_2026/8gh6_40033.map" } resolution = 3.08 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 178 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 6167 2.51 5 N 2043 2.21 5 O 2357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10785 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 7099 Classifications: {'peptide': 898} Link IDs: {'PTRANS': 43, 'TRANS': 854} Chain breaks: 2 Chain: "B" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 952 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "P" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 493 Classifications: {'DNA': 24} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 23} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 831 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 14} Link IDs: {'rna2p': 7, 'rna3p': 31} Chain breaks: 2 Chain: "T" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1378 Classifications: {'DNA': 67} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 66} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {' MG': 1, ' ZN': 2, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31 SG CYS A 114 33.451 59.687 66.101 1.00 60.08 S ATOM 57 SG CYS A 117 31.222 62.771 66.997 1.00 68.26 S ATOM 5726 SG CYS A 934 15.398 126.086 52.184 1.00 48.69 S ATOM 5752 SG CYS A 938 15.091 129.108 49.930 1.00 52.23 S ATOM 5857 SG CYS A 951 18.013 129.038 52.332 1.00 47.75 S Time building chain proxies: 1.71, per 1000 atoms: 0.16 Number of scatterers: 10785 At special positions: 0 Unit cell: (110.5, 164.424, 107.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 37 16.00 P 178 15.00 Mg 1 11.99 O 2357 8.00 N 2043 7.00 C 6167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 387.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 130 " pdb="ZN ZN A1201 " - pdb=" NE2 HIS A 135 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 117 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 114 " pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 946 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 938 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 934 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 951 " Number of angles added : 5 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 59.7% alpha, 10.7% beta 74 base pairs and 133 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.518A pdb=" N HIS A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 153 through 171 removed outlier: 3.524A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.826A pdb=" N GLY A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 198 Processing helix chain 'A' and resid 199 through 214 removed outlier: 3.852A pdb=" N GLN A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 removed outlier: 3.579A pdb=" N GLU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 343 through 357 removed outlier: 3.834A pdb=" N TYR A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Proline residue: A 353 - end of helix removed outlier: 3.539A pdb=" N ARG A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 421 through 436 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 500 through 520 removed outlier: 3.585A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.824A pdb=" N THR A 536 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 537 " --> pdb=" O PHE A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 537' Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 592 through 607 removed outlier: 3.613A pdb=" N VAL A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 604 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 655 removed outlier: 3.513A pdb=" N MET A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 745 through 748 Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 759 through 778 Processing helix chain 'A' and resid 785 through 791 removed outlier: 4.140A pdb=" N TYR A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 816 Proline residue: A 808 - end of helix Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 823 through 831 removed outlier: 3.613A pdb=" N LYS A 831 " --> pdb=" O ARG A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 849 Processing helix chain 'A' and resid 861 through 872 Processing helix chain 'A' and resid 875 through 882 removed outlier: 4.617A pdb=" N GLU A 880 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 882 " --> pdb=" O ARG A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 887 Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.422A pdb=" N ARG A 892 " --> pdb=" O THR A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 Processing helix chain 'A' and resid 899 through 911 removed outlier: 3.581A pdb=" N ILE A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 932 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 951 through 953 No H-bonds generated for 'chain 'A' and resid 951 through 953' Processing helix chain 'A' and resid 954 through 976 Processing helix chain 'A' and resid 1018 through 1032 removed outlier: 3.960A pdb=" N LYS A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TYR A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1048 through 1050 No H-bonds generated for 'chain 'A' and resid 1048 through 1050' Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1080 through 1085 Processing helix chain 'A' and resid 1086 through 1105 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113 removed outlier: 3.770A pdb=" N TRP A 112 " --> pdb=" O PHE A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 462 through 467 removed outlier: 6.888A pdb=" N CYS A 445 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A 571 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR A 447 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 467 removed outlier: 6.888A pdb=" N CYS A 445 " --> pdb=" O THR A 569 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A 571 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR A 447 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 623 through 626 Processing sheet with id=AA5, first strand: chain 'A' and resid 530 through 531 removed outlier: 4.681A pdb=" N ARG A 657 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 614 through 616 Processing sheet with id=AA7, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA8, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AA9, first strand: chain 'A' and resid 851 through 852 Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 982 removed outlier: 6.738A pdb=" N GLY A1005 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A1055 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A1007 " --> pdb=" O THR A1055 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N CYS A1057 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP A1009 " --> pdb=" O CYS A1057 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE A1059 " --> pdb=" O ASP A1009 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN A1011 " --> pdb=" O ILE A1059 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 986 through 988 removed outlier: 3.551A pdb=" N THR A 988 " --> pdb=" O GLY A 991 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 186 hydrogen bonds 372 hydrogen bond angles 0 basepair planarities 74 basepair parallelities 133 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 0.92 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: 2686 1.34 - 1.46: 3430 1.46 - 1.58: 4844 1.58 - 1.70: 353 1.70 - 1.83: 53 Bond restraints: 11366 Sorted by residual: bond pdb=" C3' DG B 30 " pdb=" O3' DG B 30 " ideal model delta sigma weight residual 1.435 1.509 -0.074 1.30e-02 5.92e+03 3.22e+01 bond pdb=" C1' DC B 25 " pdb=" N1 DC B 25 " ideal model delta sigma weight residual 1.468 1.539 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" C1' DC B 44 " pdb=" N1 DC B 44 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" C3' DT B 38 " pdb=" C2' DT B 38 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG B 30 " pdb=" C2' DG B 30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 11361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.88: 15945 3.88 - 7.76: 172 7.76 - 11.64: 20 11.64 - 15.52: 2 15.52 - 19.39: 1 Bond angle restraints: 16140 Sorted by residual: angle pdb=" CB MET A 640 " pdb=" CG MET A 640 " pdb=" SD MET A 640 " ideal model delta sigma weight residual 112.70 132.09 -19.39 3.00e+00 1.11e-01 4.18e+01 angle pdb=" CA ARG A 171 " pdb=" CB ARG A 171 " pdb=" CG ARG A 171 " ideal model delta sigma weight residual 114.10 126.21 -12.11 2.00e+00 2.50e-01 3.66e+01 angle pdb=" CA GLU A1050 " pdb=" CB GLU A1050 " pdb=" CG GLU A1050 " ideal model delta sigma weight residual 114.10 125.80 -11.70 2.00e+00 2.50e-01 3.42e+01 angle pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 112.00 104.15 7.85 1.40e+00 5.10e-01 3.15e+01 angle pdb=" C3' A R 245 " pdb=" O3' A R 245 " pdb=" P A R 246 " ideal model delta sigma weight residual 120.20 128.13 -7.93 1.50e+00 4.44e-01 2.79e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 5643 33.75 - 67.50: 718 67.50 - 101.25: 21 101.25 - 135.00: 0 135.00 - 168.75: 5 Dihedral angle restraints: 6387 sinusoidal: 3823 harmonic: 2564 Sorted by residual: dihedral pdb=" C2 TTP A1204 " pdb=" C1' TTP A1204 " pdb=" N1 TTP A1204 " pdb=" O4' TTP A1204 " ideal model delta sinusoidal sigma weight residual 301.68 150.70 150.98 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O4' A R 245 " pdb=" C1' A R 245 " pdb=" N9 A R 245 " pdb=" C4 A R 245 " ideal model delta sinusoidal sigma weight residual 254.00 175.06 78.94 1 1.70e+01 3.46e-03 2.68e+01 dihedral pdb=" CA PRO A 609 " pdb=" C PRO A 609 " pdb=" N GLU A 610 " pdb=" CA GLU A 610 " ideal model delta harmonic sigma weight residual -180.00 -155.34 -24.66 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 6384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1532 0.082 - 0.164: 257 0.164 - 0.246: 21 0.246 - 0.327: 2 0.327 - 0.409: 3 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB ILE A 911 " pdb=" CA ILE A 911 " pdb=" CG1 ILE A 911 " pdb=" CG2 ILE A 911 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" P DT P 24 " pdb=" OP1 DT P 24 " pdb=" OP2 DT P 24 " pdb=" O5' DT P 24 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C3' A R 245 " pdb=" C4' A R 245 " pdb=" O3' A R 245 " pdb=" C2' A R 245 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 1812 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 438 " 0.079 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 439 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1023 " 0.017 2.00e-02 2.50e+03 3.67e-02 2.02e+01 pdb=" CG HIS A1023 " -0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A1023 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS A1023 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A1023 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS A1023 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 197 " -0.308 9.50e-02 1.11e+02 1.39e-01 1.45e+01 pdb=" NE ARG A 197 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 197 " -0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG A 197 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 197 " -0.002 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 305 2.68 - 3.24: 8573 3.24 - 3.79: 18741 3.79 - 4.35: 24915 4.35 - 4.90: 36675 Nonbonded interactions: 89209 Sorted by model distance: nonbonded pdb=" O PHE A 530 " pdb="MG MG A1203 " model vdw 2.128 2.170 nonbonded pdb=" OD2 ASP A 628 " pdb="MG MG A1203 " model vdw 2.159 2.170 nonbonded pdb="MG MG A1203 " pdb=" O1A TTP A1204 " model vdw 2.213 2.170 nonbonded pdb=" O LYS A 131 " pdb=" OG1 THR A 139 " model vdw 2.332 3.040 nonbonded pdb=" O ILE A 497 " pdb=" O2' A R 250 " model vdw 2.346 3.040 ... (remaining 89204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.980 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.007 0.114 11374 Z= 0.509 Angle : 1.162 19.394 16145 Z= 0.768 Chirality : 0.062 0.409 1815 Planarity : 0.010 0.139 1449 Dihedral : 22.495 168.754 4733 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.02 % Favored : 97.87 % Rotamer: Outliers : 0.13 % Allowed : 11.42 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.25), residues: 892 helix: -0.88 (0.20), residues: 461 sheet: -0.10 (0.59), residues: 81 loop : -0.31 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG A 197 TYR 0.054 0.004 TYR A 202 PHE 0.047 0.004 PHE A 180 TRP 0.032 0.003 TRP A1061 HIS 0.052 0.004 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.51 (11366) covalent geometry : angle 1.16009 / 0.77 (16140) hydrogen bonds : bond 0.15751 / 10.88 ( 567) hydrogen bonds : angle 5.86773 / 4.18 ( 1449) metal coordination : bond 0.01730 / 1.13 ( 8) metal coordination : angle 4.32565 / 1.96 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.207 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1406 time to fit residues: 18.6134 Evaluate side-chains 76 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 GLN A 678 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.179276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134145 restraints weight = 14594.236| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.46 r_work: 0.3342 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11374 Z= 0.162 Angle : 0.698 8.430 16145 Z= 0.396 Chirality : 0.047 0.271 1815 Planarity : 0.006 0.055 1449 Dihedral : 24.950 166.762 2991 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.68 % Favored : 98.21 % Rotamer: Outliers : 2.12 % Allowed : 9.03 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 892 helix: 0.54 (0.23), residues: 471 sheet: -0.21 (0.55), residues: 87 loop : -0.14 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 418 TYR 0.017 0.002 TYR A 202 PHE 0.012 0.001 PHE A 449 TRP 0.019 0.002 TRP A1061 HIS 0.009 0.002 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (11366) covalent geometry : angle 0.69664 / 0.40 (16140) hydrogen bonds : bond 0.05471 / 3.64 ( 567) hydrogen bonds : angle 4.06957 / 2.87 ( 1449) metal coordination : bond 0.00650 / 0.42 ( 8) metal coordination : angle 2.33043 / 1.01 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6739 (ttm-80) cc_final: 0.6280 (tpt90) REVERT: A 540 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7391 (tt0) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 0.1079 time to fit residues: 12.7157 Evaluate side-chains 81 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1055 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 910 HIS A1096 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.129500 restraints weight = 14563.736| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.53 r_work: 0.3262 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11374 Z= 0.186 Angle : 0.703 8.738 16145 Z= 0.393 Chirality : 0.047 0.310 1815 Planarity : 0.006 0.045 1449 Dihedral : 25.270 165.981 2991 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.31 % Rotamer: Outliers : 2.79 % Allowed : 11.16 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.28), residues: 892 helix: 0.88 (0.23), residues: 474 sheet: 0.47 (0.62), residues: 63 loop : -0.26 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 584 TYR 0.021 0.002 TYR A 202 PHE 0.015 0.002 PHE A 749 TRP 0.019 0.002 TRP A1061 HIS 0.011 0.002 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (11366) covalent geometry : angle 0.70045 / 0.39 (16140) hydrogen bonds : bond 0.05583 / 3.68 ( 567) hydrogen bonds : angle 3.81167 / 2.70 ( 1449) metal coordination : bond 0.01026 / 0.67 ( 8) metal coordination : angle 3.15972 / 1.63 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.251 Fit side-chains REVERT: A 171 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6260 (tpt90) outliers start: 21 outliers final: 14 residues processed: 85 average time/residue: 0.1027 time to fit residues: 12.1051 Evaluate side-chains 79 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 686 ASN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1055 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 0.0000 chunk 90 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 870 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126712 restraints weight = 14561.603| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.38 r_work: 0.3261 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11374 Z= 0.234 Angle : 0.735 9.486 16145 Z= 0.407 Chirality : 0.049 0.332 1815 Planarity : 0.006 0.046 1449 Dihedral : 25.506 167.323 2991 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.53 % Rotamer: Outliers : 3.05 % Allowed : 12.35 % Favored : 84.59 % 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: 0.27 (0.28), residues: 892 helix: 0.77 (0.23), residues: 468 sheet: 0.28 (0.62), residues: 63 loop : -0.52 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 584 TYR 0.020 0.002 TYR A 788 PHE 0.018 0.002 PHE A 749 TRP 0.020 0.002 TRP A1061 HIS 0.008 0.002 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.23 (11366) covalent geometry : angle 0.73270 / 0.41 (16140) hydrogen bonds : bond 0.05909 / 3.88 ( 567) hydrogen bonds : angle 3.93244 / 2.80 ( 1449) metal coordination : bond 0.01309 / 0.85 ( 8) metal coordination : angle 3.15338 / 1.74 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.207 Fit side-chains REVERT: A 171 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6369 (tpt90) REVERT: A 617 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: A 1038 GLU cc_start: 0.5616 (mm-30) cc_final: 0.5347 (mt-10) outliers start: 23 outliers final: 17 residues processed: 82 average time/residue: 0.1167 time to fit residues: 13.0933 Evaluate side-chains 80 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1036 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.174545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127618 restraints weight = 14386.511| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.32 r_work: 0.3296 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11374 Z= 0.198 Angle : 0.684 9.490 16145 Z= 0.381 Chirality : 0.046 0.313 1815 Planarity : 0.005 0.042 1449 Dihedral : 25.537 167.677 2991 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.35 % Favored : 97.53 % Rotamer: Outliers : 3.19 % Allowed : 13.55 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 892 helix: 0.99 (0.24), residues: 474 sheet: 0.31 (0.61), residues: 63 loop : -0.50 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 764 TYR 0.015 0.002 TYR A 788 PHE 0.015 0.002 PHE A 749 TRP 0.019 0.001 TRP A1061 HIS 0.008 0.002 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (11366) covalent geometry : angle 0.68188 / 0.38 (16140) hydrogen bonds : bond 0.05328 / 3.50 ( 567) hydrogen bonds : angle 3.77922 / 2.69 ( 1449) metal coordination : bond 0.01407 / 0.90 ( 8) metal coordination : angle 2.92762 / 1.50 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.316 Fit side-chains REVERT: A 171 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6379 (tpt90) REVERT: A 418 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.6196 (ttt180) REVERT: A 540 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 617 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: A 1038 GLU cc_start: 0.5614 (mm-30) cc_final: 0.5349 (mt-10) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.1235 time to fit residues: 13.9995 Evaluate side-chains 84 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1040 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 751 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.124869 restraints weight = 14436.466| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.41 r_work: 0.3240 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 11374 Z= 0.300 Angle : 0.800 9.771 16145 Z= 0.434 Chirality : 0.052 0.365 1815 Planarity : 0.007 0.055 1449 Dihedral : 25.782 167.177 2991 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.75 % Rotamer: Outliers : 3.72 % Allowed : 13.15 % Favored : 83.13 % 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: -0.09 (0.27), residues: 892 helix: 0.53 (0.23), residues: 477 sheet: 0.11 (0.59), residues: 63 loop : -0.80 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 587 TYR 0.022 0.003 TYR A 788 PHE 0.018 0.002 PHE A 749 TRP 0.024 0.002 TRP A1061 HIS 0.010 0.002 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.30 (11366) covalent geometry : angle 0.79716 / 0.43 (16140) hydrogen bonds : bond 0.06784 / 4.47 ( 567) hydrogen bonds : angle 4.09658 / 2.92 ( 1449) metal coordination : bond 0.01802 / 1.17 ( 8) metal coordination : angle 3.93567 / 2.23 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.282 Fit side-chains REVERT: A 171 ARG cc_start: 0.7198 (ttm-80) cc_final: 0.6471 (tpt90) REVERT: A 418 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5982 (ttt180) REVERT: A 540 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: A 617 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: A 1038 GLU cc_start: 0.5656 (mm-30) cc_final: 0.5313 (mt-10) REVERT: A 1046 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.4876 (pp) outliers start: 28 outliers final: 19 residues processed: 85 average time/residue: 0.1231 time to fit residues: 14.2382 Evaluate side-chains 86 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 617 GLU Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 99 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 0.0170 chunk 57 optimal weight: 0.2980 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.177134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130296 restraints weight = 14492.050| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.38 r_work: 0.3314 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11374 Z= 0.133 Angle : 0.624 9.671 16145 Z= 0.350 Chirality : 0.043 0.283 1815 Planarity : 0.005 0.042 1449 Dihedral : 25.530 168.792 2991 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.68 % Favored : 98.21 % Rotamer: Outliers : 2.39 % Allowed : 14.08 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 892 helix: 1.32 (0.24), residues: 473 sheet: 0.06 (0.60), residues: 65 loop : -0.37 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 611 TYR 0.010 0.001 TYR A 563 PHE 0.012 0.001 PHE A 968 TRP 0.013 0.001 TRP A 701 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (11366) covalent geometry : angle 0.62183 / 0.35 (16140) hydrogen bonds : bond 0.04373 / 2.85 ( 567) hydrogen bonds : angle 3.58058 / 2.55 ( 1449) metal coordination : bond 0.01162 / 0.74 ( 8) metal coordination : angle 2.80540 / 1.26 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.323 Fit side-chains REVERT: A 171 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6402 (tpt90) REVERT: A 540 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: A 1038 GLU cc_start: 0.5803 (mm-30) cc_final: 0.5537 (mt-10) REVERT: A 1046 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4855 (pp) outliers start: 18 outliers final: 12 residues processed: 88 average time/residue: 0.1390 time to fit residues: 16.4061 Evaluate side-chains 83 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 GLN A 744 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128903 restraints weight = 14511.401| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.40 r_work: 0.3281 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11374 Z= 0.158 Angle : 0.637 9.861 16145 Z= 0.355 Chirality : 0.044 0.294 1815 Planarity : 0.005 0.043 1449 Dihedral : 25.542 168.397 2991 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.47 % Favored : 97.42 % Rotamer: Outliers : 2.52 % Allowed : 14.61 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 892 helix: 1.33 (0.24), residues: 474 sheet: 0.15 (0.61), residues: 65 loop : -0.36 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 611 TYR 0.013 0.002 TYR A 788 PHE 0.012 0.001 PHE A 968 TRP 0.015 0.001 TRP A1061 HIS 0.008 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (11366) covalent geometry : angle 0.63563 / 0.36 (16140) hydrogen bonds : bond 0.04798 / 3.14 ( 567) hydrogen bonds : angle 3.61894 / 2.58 ( 1449) metal coordination : bond 0.01336 / 0.86 ( 8) metal coordination : angle 2.56390 / 1.34 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.338 Fit side-chains REVERT: A 157 ILE cc_start: 0.7465 (mt) cc_final: 0.7227 (mt) REVERT: A 171 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6424 (tpt90) REVERT: A 540 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7144 (tt0) REVERT: A 1046 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4864 (pp) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.1316 time to fit residues: 14.8243 Evaluate side-chains 84 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 776 GLN Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 979 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.0030 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.178952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.132757 restraints weight = 14483.864| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.37 r_work: 0.3343 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11374 Z= 0.122 Angle : 0.588 9.975 16145 Z= 0.331 Chirality : 0.041 0.264 1815 Planarity : 0.004 0.045 1449 Dihedral : 25.364 170.166 2991 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.91 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 15.54 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 892 helix: 1.67 (0.24), residues: 474 sheet: 0.18 (0.61), residues: 65 loop : -0.28 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 611 TYR 0.010 0.001 TYR A 350 PHE 0.010 0.001 PHE A 968 TRP 0.013 0.001 TRP A 701 HIS 0.004 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (11366) covalent geometry : angle 0.58712 / 0.33 (16140) hydrogen bonds : bond 0.03874 / 2.50 ( 567) hydrogen bonds : angle 3.42034 / 2.44 ( 1449) metal coordination : bond 0.00986 / 0.63 ( 8) metal coordination : angle 2.13976 / 0.96 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.7028 (ttm-80) cc_final: 0.6501 (ttp80) REVERT: A 515 ASP cc_start: 0.8508 (t70) cc_final: 0.8122 (t70) REVERT: A 540 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7112 (tt0) REVERT: A 1046 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4868 (pp) outliers start: 13 outliers final: 10 residues processed: 89 average time/residue: 0.1397 time to fit residues: 16.9883 Evaluate side-chains 84 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 70 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 98 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.131417 restraints weight = 14521.591| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.41 r_work: 0.3312 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11374 Z= 0.139 Angle : 0.592 10.063 16145 Z= 0.334 Chirality : 0.042 0.282 1815 Planarity : 0.005 0.044 1449 Dihedral : 25.345 170.696 2991 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.24 % Favored : 97.65 % Rotamer: Outliers : 1.99 % Allowed : 15.27 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.29), residues: 892 helix: 1.68 (0.24), residues: 474 sheet: 0.25 (0.62), residues: 65 loop : -0.24 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 611 TYR 0.010 0.001 TYR A 788 PHE 0.011 0.001 PHE A 968 TRP 0.013 0.001 TRP A1061 HIS 0.005 0.001 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (11366) covalent geometry : angle 0.59136 / 0.33 (16140) hydrogen bonds : bond 0.04291 / 2.79 ( 567) hydrogen bonds : angle 3.43462 / 2.45 ( 1449) metal coordination : bond 0.01022 / 0.66 ( 8) metal coordination : angle 2.01483 / 1.02 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6446 (ttp80) REVERT: A 515 ASP cc_start: 0.8517 (t70) cc_final: 0.8122 (t70) REVERT: A 540 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: A 1046 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4802 (pp) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1271 time to fit residues: 13.9011 Evaluate side-chains 82 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 0.0770 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.127289 restraints weight = 14564.845| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.38 r_work: 0.3268 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11374 Z= 0.202 Angle : 0.669 10.112 16145 Z= 0.370 Chirality : 0.045 0.319 1815 Planarity : 0.006 0.041 1449 Dihedral : 25.484 171.072 2991 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.09 % Rotamer: Outliers : 2.52 % Allowed : 14.87 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.28), residues: 892 helix: 1.30 (0.24), residues: 476 sheet: 0.31 (0.61), residues: 63 loop : -0.49 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 611 TYR 0.017 0.002 TYR A 788 PHE 0.014 0.002 PHE A 749 TRP 0.017 0.002 TRP A1061 HIS 0.009 0.002 HIS A1096 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (11366) covalent geometry : angle 0.66685 / 0.37 (16140) hydrogen bonds : bond 0.05333 / 3.49 ( 567) hydrogen bonds : angle 3.65782 / 2.61 ( 1449) metal coordination : bond 0.01256 / 0.81 ( 8) metal coordination : angle 2.89673 / 1.64 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.45 seconds wall clock time: 53 minutes 57.91 seconds (3237.91 seconds total)