Starting phenix.real_space_refine on Wed Aug 5 17:08:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl4_49517/08_2026/9nl4_49517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl4_49517/08_2026/9nl4_49517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2026/9nl4_49517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2026/9nl4_49517.map" model { file = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2026/9nl4_49517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2026/9nl4_49517.cif" } resolution = 4.6 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 79 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 92 5.49 5 S 50 5.16 5 C 6505 2.51 5 N 1914 2.21 5 O 2183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8854 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1049} Chain breaks: 1 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "P" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "R" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "T" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 764 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 107 SG CYS A 14 53.920 118.068 37.585 1.00311.12 S ATOM 131 SG CYS A 17 51.957 121.288 37.485 1.00309.26 S ATOM 340 SG CYS A 44 70.257 105.804 34.913 1.00310.09 S ATOM 360 SG CYS A 47 70.249 102.744 33.255 1.00303.90 S ATOM 489 SG CYS A 64 73.191 103.704 34.300 1.00266.14 S ATOM 594 SG CYS A 78 65.992 80.151 27.532 1.00259.28 S ATOM 616 SG CYS A 81 63.958 82.707 28.114 1.00256.46 S ATOM 7380 SG CYS A 941 65.924 131.463 68.418 1.00250.33 S ATOM 7405 SG CYS A 944 67.371 133.016 71.384 1.00232.07 S ATOM 7509 SG CYS A 958 63.695 132.070 71.514 1.00268.84 S Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10748 At special positions: 0 Unit cell: (100.32, 150.48, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 50 16.00 P 92 15.00 O 2183 8.00 N 1914 7.00 C 6505 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: 0.99 Conformation dependent library (CDL) restraints added in 413.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 30 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 35 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 17 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 14 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 60 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 64 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 44 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 47 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" ND1 HIS A 94 " pdb="ZN ZN A2002 " - pdb=" ND1 HIS A 99 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 78 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A 953 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 944 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 941 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 958 " Number of angles added : 9 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 54.4% alpha, 8.9% beta 36 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 53 through 64 Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.262A pdb=" N ASP A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 203 through 220 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.579A pdb=" N ILE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 256 Processing helix chain 'A' and resid 284 through 301 Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.931A pdb=" N ILE A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.695A pdb=" N GLU A 418 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 446 through 464 Processing helix chain 'A' and resid 477 through 497 removed outlier: 3.665A pdb=" N GLU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 removed outlier: 3.541A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 568 through 589 removed outlier: 4.392A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) Proline residue: A 580 - end of helix Processing helix chain 'A' and resid 614 through 633 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 694 through 708 removed outlier: 3.700A pdb=" N LYS A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 735 removed outlier: 4.881A pdb=" N ILE A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.967A pdb=" N LEU A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 758 Processing helix chain 'A' and resid 764 through 770 removed outlier: 4.008A pdb=" N ILE A 768 " --> pdb=" O CYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 799 Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 813 through 826 removed outlier: 4.444A pdb=" N GLU A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 888 through 893 Processing helix chain 'A' and resid 899 through 905 removed outlier: 4.103A pdb=" N GLN A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 926 through 932 Processing helix chain 'A' and resid 959 through 961 No H-bonds generated for 'chain 'A' and resid 959 through 961' Processing helix chain 'A' and resid 962 through 983 removed outlier: 3.749A pdb=" N GLU A 982 " --> pdb=" O ARG A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1041 Processing helix chain 'A' and resid 1044 through 1051 Processing helix chain 'A' and resid 1071 through 1081 Processing helix chain 'A' and resid 1083 through 1120 removed outlier: 4.575A pdb=" N GLY A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASN A1116 " --> pdb=" O ILE A1112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 5.119A pdb=" N THR A 3 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN A 43 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE A 5 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 444 removed outlier: 5.006A pdb=" N LEU A 423 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 439 through 444 removed outlier: 5.006A pdb=" N LEU A 423 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 603 through 604 removed outlier: 3.836A pdb=" N LEU A 608 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 612 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 501 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 removed outlier: 3.836A pdb=" N LEU A 608 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 612 " --> pdb=" O GLY A 501 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 501 " --> pdb=" O SER A 612 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 677 through 679 Processing sheet with id=AA7, first strand: chain 'A' and resid 840 through 841 Processing sheet with id=AA8, first strand: chain 'A' and resid 1005 through 1009 removed outlier: 3.608A pdb=" N LEU A1005 " --> pdb=" O VAL A1016 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2937 1.33 - 1.45: 2261 1.45 - 1.57: 5705 1.57 - 1.69: 180 1.69 - 1.81: 73 Bond restraints: 11156 Sorted by residual: bond pdb=" P DT B 45 " pdb=" O5' DT B 45 " ideal model delta sigma weight residual 1.593 1.658 -0.065 1.00e-02 1.00e+04 4.17e+01 bond pdb=" C3' DA B 31 " pdb=" C2' DA B 31 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C1' DT B 42 " pdb=" N1 DT B 42 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" P DC B 44 " pdb=" O5' DC B 44 " ideal model delta sigma weight residual 1.593 1.624 -0.031 1.00e-02 1.00e+04 9.83e+00 bond pdb=" C1' DT B 55 " pdb=" N1 DT B 55 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.28e+00 ... (remaining 11151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.17: 15460 8.17 - 16.35: 5 16.35 - 24.52: 3 24.52 - 32.69: 3 32.69 - 40.87: 3 Bond angle restraints: 15474 Sorted by residual: angle pdb=" O3' DC B 44 " pdb=" P DT B 45 " pdb=" O5' DT B 45 " ideal model delta sigma weight residual 104.00 69.91 34.09 1.90e+00 2.77e-01 3.22e+02 angle pdb=" OP1 DC B 57 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 120.00 79.13 40.87 3.00e+00 1.11e-01 1.86e+02 angle pdb=" OP2 DC B 57 " pdb=" P DC B 57 " pdb=" O5' DC B 57 " ideal model delta sigma weight residual 108.00 74.11 33.89 3.00e+00 1.11e-01 1.28e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP1 DC B 57 " ideal model delta sigma weight residual 108.00 75.75 32.25 3.00e+00 1.11e-01 1.16e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 108.00 135.40 -27.40 3.00e+00 1.11e-01 8.34e+01 ... (remaining 15469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 6103 35.17 - 70.34: 467 70.34 - 105.51: 19 105.51 - 140.67: 0 140.67 - 175.84: 4 Dihedral angle restraints: 6593 sinusoidal: 3365 harmonic: 3228 Sorted by residual: dihedral pdb=" CA PRO A 115 " pdb=" C PRO A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta harmonic sigma weight residual -180.00 -134.46 -45.54 0 5.00e+00 4.00e-02 8.30e+01 dihedral pdb=" CA CYS A 59 " pdb=" C CYS A 59 " pdb=" N HIS A 60 " pdb=" CA HIS A 60 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PRO A 477 " pdb=" C PRO A 477 " pdb=" N GLY A 478 " pdb=" CA GLY A 478 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.456: 1728 0.456 - 0.912: 9 0.912 - 1.368: 0 1.368 - 1.824: 0 1.824 - 2.280: 2 Chirality restraints: 1739 Sorted by residual: chirality pdb=" P DT B 45 " pdb=" OP1 DT B 45 " pdb=" OP2 DT B 45 " pdb=" O5' DT B 45 " both_signs ideal model delta sigma weight residual True 2.34 0.05 2.28 2.00e-01 2.50e+01 1.30e+02 chirality pdb=" P DA B 29 " pdb=" OP1 DA B 29 " pdb=" OP2 DA B 29 " pdb=" O5' DA B 29 " both_signs ideal model delta sigma weight residual True 2.34 0.41 1.93 2.00e-01 2.50e+01 9.28e+01 chirality pdb=" P DC T 9 " pdb=" OP1 DC T 9 " pdb=" OP2 DC T 9 " pdb=" O5' DC T 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 1736 not shown) Planarity restraints: 1653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1113 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C GLY A1113 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY A1113 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A1114 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 114 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO A 115 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 720 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C LEU A 720 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 720 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 721 " -0.011 2.00e-02 2.50e+03 ... (remaining 1650 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 59 2.28 - 2.93: 5755 2.93 - 3.59: 18839 3.59 - 4.24: 28431 4.24 - 4.90: 42956 Nonbonded interactions: 96040 Sorted by model distance: nonbonded pdb=" OG SER A 652 " pdb=" P DT B 45 " model vdw 1.621 3.400 nonbonded pdb=" O ILE A 251 " pdb=" OG1 THR A 254 " model vdw 1.853 3.040 nonbonded pdb=" O SER A 332 " pdb=" OG1 THR A 336 " model vdw 1.924 3.040 nonbonded pdb=" OG SER A 647 " pdb=" OG1 THR A 654 " model vdw 1.932 3.040 nonbonded pdb=" O ILE A 108 " pdb=" OG SER A 111 " model vdw 1.932 3.040 ... (remaining 96035 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 group one per residue 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.040 Find NCS groups from input model: 0.050 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.009 0.491 11172 Z= 0.454 Angle : 1.175 40.869 15483 Z= 0.657 Chirality : 0.096 2.280 1739 Planarity : 0.006 0.059 1653 Dihedral : 21.029 175.842 4493 Min Nonbonded Distance : 1.621 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.82 % Allowed : 13.15 % Favored : 86.04 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.58 (0.24), residues: 1103 helix: -0.51 (0.22), residues: 523 sheet: -2.71 (0.56), residues: 67 loop : -2.93 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 844 TYR 0.013 0.002 TYR A1024 PHE 0.021 0.002 PHE A1094 TRP 0.018 0.002 TRP A 661 HIS 0.012 0.002 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.42 (11156) covalent geometry : angle 1.13234 / 0.65 (15474) hydrogen bonds : bond 0.18041 / 12.61 ( 528) hydrogen bonds : angle 7.73160 / 5.61 ( 1483) metal coordination : bond 0.16786 / 8.49 ( 16) metal coordination : angle 13.00655 / 7.15 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6475 (mpp) cc_final: 0.5702 (mpp) REVERT: A 367 MET cc_start: 0.9632 (mmm) cc_final: 0.9406 (mpp) REVERT: A 373 MET cc_start: 0.8582 (mmp) cc_final: 0.7964 (mmm) REVERT: A 483 LEU cc_start: 0.9698 (mt) cc_final: 0.9470 (mt) REVERT: A 756 TRP cc_start: 0.9119 (m-10) cc_final: 0.8914 (m-10) REVERT: A 975 MET cc_start: 0.9472 (mmp) cc_final: 0.9252 (mmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1003 time to fit residues: 11.4377 Evaluate side-chains 51 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS A 369 ASN A 458 ASN A 589 ASN A 630 ASN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.050093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030393 restraints weight = 95988.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031358 restraints weight = 66576.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031949 restraints weight = 51846.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032445 restraints weight = 43933.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032747 restraints weight = 39062.886| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11172 Z= 0.211 Angle : 1.026 38.816 15483 Z= 0.483 Chirality : 0.067 1.934 1739 Planarity : 0.006 0.098 1653 Dihedral : 24.820 176.434 2219 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.52 % Favored : 89.66 % Rotamer: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.65 (0.25), residues: 1103 helix: 0.32 (0.22), residues: 536 sheet: -2.93 (0.54), residues: 75 loop : -2.44 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 241 TYR 0.014 0.002 TYR A 330 PHE 0.013 0.002 PHE A 357 TRP 0.016 0.002 TRP A 406 HIS 0.007 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.21 (11156) covalent geometry : angle 1.01038 / 0.48 (15474) hydrogen bonds : bond 0.07522 / 5.52 ( 528) hydrogen bonds : angle 6.06958 / 4.37 ( 1483) metal coordination : bond 0.02419 / 1.08 ( 16) metal coordination : angle 7.41835 / 4.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9644 (mmp) cc_final: 0.9322 (ptm) REVERT: A 257 MET cc_start: 0.6785 (mpp) cc_final: 0.6218 (mpp) REVERT: A 373 MET cc_start: 0.8952 (mmp) cc_final: 0.8474 (mmm) REVERT: A 483 LEU cc_start: 0.9742 (mt) cc_final: 0.9494 (mt) REVERT: A 569 MET cc_start: 0.9186 (mmp) cc_final: 0.8795 (mmm) REVERT: A 876 MET cc_start: 0.9667 (tpt) cc_final: 0.9319 (mtt) REVERT: A 975 MET cc_start: 0.9517 (mmp) cc_final: 0.9300 (mmm) REVERT: A 1078 THR cc_start: 0.9187 (t) cc_final: 0.8983 (p) REVERT: A 1103 ILE cc_start: 0.9705 (mm) cc_final: 0.9479 (mm) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.0837 time to fit residues: 8.8423 Evaluate side-chains 48 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 110 optimal weight: 40.0000 chunk 82 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 544 HIS ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.049106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.029788 restraints weight = 96793.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.030735 restraints weight = 65522.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031459 restraints weight = 50636.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031927 restraints weight = 42175.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.032215 restraints weight = 37466.141| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11172 Z= 0.226 Angle : 1.012 38.522 15483 Z= 0.478 Chirality : 0.064 1.863 1739 Planarity : 0.006 0.061 1653 Dihedral : 24.619 176.646 2219 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.07 % Favored : 90.21 % Rotamer: Outliers : 0.10 % Allowed : 4.97 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.24 (0.25), residues: 1103 helix: 0.60 (0.22), residues: 534 sheet: -2.69 (0.51), residues: 77 loop : -2.16 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 285 TYR 0.015 0.002 TYR A 843 PHE 0.014 0.002 PHE A 357 TRP 0.015 0.002 TRP A 406 HIS 0.008 0.002 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.23 (11156) covalent geometry : angle 1.00141 / 0.48 (15474) hydrogen bonds : bond 0.06380 / 4.67 ( 528) hydrogen bonds : angle 5.71807 / 4.15 ( 1483) metal coordination : bond 0.02310 / 1.04 ( 16) metal coordination : angle 6.21752 / 3.22 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6802 (mpp) cc_final: 0.6037 (mpp) REVERT: A 367 MET cc_start: 0.9702 (mmp) cc_final: 0.9468 (mmt) REVERT: A 373 MET cc_start: 0.8846 (mmp) cc_final: 0.8365 (mmm) REVERT: A 483 LEU cc_start: 0.9796 (mt) cc_final: 0.9584 (mt) REVERT: A 569 MET cc_start: 0.9201 (mmp) cc_final: 0.8760 (mmm) REVERT: A 618 MET cc_start: 0.9220 (tpp) cc_final: 0.8434 (tpp) REVERT: A 876 MET cc_start: 0.9732 (tpt) cc_final: 0.9409 (mtt) REVERT: A 975 MET cc_start: 0.9564 (mmp) cc_final: 0.9350 (mmm) REVERT: A 1103 ILE cc_start: 0.9711 (mm) cc_final: 0.9480 (mm) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1093 time to fit residues: 10.6878 Evaluate side-chains 48 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 20.0000 chunk 71 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 438 ASN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.050233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.030302 restraints weight = 94799.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.031328 restraints weight = 64664.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.032044 restraints weight = 49935.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032478 restraints weight = 41783.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.032688 restraints weight = 37162.969| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.130 11172 Z= 0.161 Angle : 0.983 38.272 15483 Z= 0.452 Chirality : 0.064 1.877 1739 Planarity : 0.005 0.088 1653 Dihedral : 24.588 175.858 2219 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.62 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.92 (0.26), residues: 1103 helix: 0.93 (0.22), residues: 535 sheet: -2.56 (0.51), residues: 82 loop : -2.08 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 387 TYR 0.016 0.002 TYR A 330 PHE 0.013 0.002 PHE A 403 TRP 0.014 0.001 TRP A 822 HIS 0.005 0.001 HIS A 953 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.16 (11156) covalent geometry : angle 0.96077 / 0.45 (15474) hydrogen bonds : bond 0.05389 / 3.97 ( 528) hydrogen bonds : angle 5.37953 / 3.91 ( 1483) metal coordination : bond 0.04434 / 1.93 ( 16) metal coordination : angle 8.71704 / 4.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6888 (mpp) cc_final: 0.6239 (mpp) REVERT: A 367 MET cc_start: 0.9669 (mmp) cc_final: 0.9427 (mmt) REVERT: A 373 MET cc_start: 0.8675 (mmm) cc_final: 0.8459 (mmm) REVERT: A 569 MET cc_start: 0.9140 (mmp) cc_final: 0.8668 (mmm) REVERT: A 610 MET cc_start: 0.8894 (tpt) cc_final: 0.8644 (tpt) REVERT: A 876 MET cc_start: 0.9751 (tpt) cc_final: 0.9407 (mtt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0837 time to fit residues: 8.4820 Evaluate side-chains 44 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 25 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 369 ASN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.048922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.029157 restraints weight = 96137.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.030105 restraints weight = 65654.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030757 restraints weight = 50973.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.031141 restraints weight = 43050.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.031307 restraints weight = 38689.634| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 11172 Z= 0.194 Angle : 0.971 38.108 15483 Z= 0.448 Chirality : 0.062 1.860 1739 Planarity : 0.005 0.052 1653 Dihedral : 24.493 176.041 2219 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.61 % Favored : 90.84 % Rotamer: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.26), residues: 1103 helix: 0.94 (0.22), residues: 541 sheet: -2.58 (0.51), residues: 78 loop : -1.96 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 387 TYR 0.015 0.002 TYR A 330 PHE 0.009 0.001 PHE A 628 TRP 0.010 0.001 TRP A 822 HIS 0.005 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (11156) covalent geometry : angle 0.95567 / 0.45 (15474) hydrogen bonds : bond 0.05524 / 4.01 ( 528) hydrogen bonds : angle 5.33293 / 3.85 ( 1483) metal coordination : bond 0.03733 / 1.51 ( 16) metal coordination : angle 7.25781 / 3.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6877 (mpp) cc_final: 0.6467 (mpp) REVERT: A 373 MET cc_start: 0.8779 (mmm) cc_final: 0.8555 (mmm) REVERT: A 569 MET cc_start: 0.9101 (mmp) cc_final: 0.8623 (mmm) REVERT: A 876 MET cc_start: 0.9774 (tpt) cc_final: 0.9427 (mtt) REVERT: A 1082 MET cc_start: 0.8813 (pmm) cc_final: 0.8446 (pmm) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.0820 time to fit residues: 7.5455 Evaluate side-chains 42 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 HIS ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029702 restraints weight = 96501.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.030692 restraints weight = 65020.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031363 restraints weight = 50273.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.031788 restraints weight = 42030.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.031975 restraints weight = 37423.297| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 11172 Z= 0.165 Angle : 0.948 37.886 15483 Z= 0.437 Chirality : 0.062 1.870 1739 Planarity : 0.005 0.053 1653 Dihedral : 24.456 175.389 2219 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.16 % Favored : 91.30 % Rotamer: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.64 (0.26), residues: 1103 helix: 0.97 (0.23), residues: 541 sheet: -2.33 (0.51), residues: 82 loop : -1.73 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 168 TYR 0.017 0.002 TYR A 330 PHE 0.009 0.001 PHE A 357 TRP 0.013 0.001 TRP A 822 HIS 0.005 0.001 HIS A1039 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (11156) covalent geometry : angle 0.93671 / 0.44 (15474) hydrogen bonds : bond 0.04848 / 3.53 ( 528) hydrogen bonds : angle 5.18077 / 3.76 ( 1483) metal coordination : bond 0.02955 / 1.22 ( 16) metal coordination : angle 6.16781 / 3.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7045 (mpp) cc_final: 0.6656 (mpp) REVERT: A 373 MET cc_start: 0.8685 (mmm) cc_final: 0.8476 (mmm) REVERT: A 569 MET cc_start: 0.9123 (mmp) cc_final: 0.8642 (mmm) REVERT: A 876 MET cc_start: 0.9782 (tpt) cc_final: 0.9405 (mtt) REVERT: A 1082 MET cc_start: 0.8836 (pmm) cc_final: 0.8510 (pmm) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.1006 time to fit residues: 9.0264 Evaluate side-chains 41 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.0770 chunk 28 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 overall best weight: 3.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.028876 restraints weight = 97970.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.029819 restraints weight = 65649.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030470 restraints weight = 50647.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030855 restraints weight = 42518.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.031036 restraints weight = 38006.093| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11172 Z= 0.199 Angle : 0.973 37.987 15483 Z= 0.450 Chirality : 0.062 1.862 1739 Planarity : 0.005 0.052 1653 Dihedral : 24.381 175.748 2219 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.56 (0.26), residues: 1103 helix: 1.08 (0.22), residues: 539 sheet: -2.31 (0.52), residues: 81 loop : -1.72 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 781 TYR 0.017 0.002 TYR A 769 PHE 0.011 0.002 PHE A 141 TRP 0.010 0.001 TRP A 822 HIS 0.008 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (11156) covalent geometry : angle 0.95517 / 0.45 (15474) hydrogen bonds : bond 0.05349 / 3.82 ( 528) hydrogen bonds : angle 5.19576 / 3.76 ( 1483) metal coordination : bond 0.02645 / 1.16 ( 16) metal coordination : angle 7.76447 / 4.16 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7154 (mpp) cc_final: 0.6803 (mpp) REVERT: A 373 MET cc_start: 0.8689 (mmm) cc_final: 0.8452 (mmm) REVERT: A 569 MET cc_start: 0.9138 (mmp) cc_final: 0.8684 (mmm) REVERT: A 618 MET cc_start: 0.9438 (tpp) cc_final: 0.8620 (tpp) REVERT: A 756 TRP cc_start: 0.8932 (m-10) cc_final: 0.8625 (m-90) REVERT: A 876 MET cc_start: 0.9798 (tpt) cc_final: 0.9407 (mtt) REVERT: A 1082 MET cc_start: 0.8793 (pmm) cc_final: 0.8421 (pmm) REVERT: A 1103 ILE cc_start: 0.9763 (mt) cc_final: 0.9513 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0885 time to fit residues: 7.3644 Evaluate side-chains 38 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN A 138 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028913 restraints weight = 96299.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.029850 restraints weight = 64280.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.030487 restraints weight = 50172.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.030766 restraints weight = 42241.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.031083 restraints weight = 38392.132| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 11172 Z= 0.167 Angle : 0.948 37.762 15483 Z= 0.434 Chirality : 0.062 1.872 1739 Planarity : 0.005 0.053 1653 Dihedral : 24.324 175.695 2219 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.58 (0.26), residues: 1103 helix: 1.06 (0.22), residues: 544 sheet: -2.62 (0.51), residues: 84 loop : -1.69 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 168 TYR 0.014 0.002 TYR A 988 PHE 0.010 0.001 PHE A 255 TRP 0.013 0.001 TRP A 822 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (11156) covalent geometry : angle 0.93226 / 0.43 (15474) hydrogen bonds : bond 0.04752 / 3.42 ( 528) hydrogen bonds : angle 5.07367 / 3.67 ( 1483) metal coordination : bond 0.05061 / 1.96 ( 16) metal coordination : angle 7.24610 / 3.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6776 (mpp) cc_final: 0.6467 (mpp) REVERT: A 373 MET cc_start: 0.8650 (mmm) cc_final: 0.8406 (mmm) REVERT: A 569 MET cc_start: 0.9098 (mmp) cc_final: 0.8655 (mmm) REVERT: A 756 TRP cc_start: 0.8954 (m-10) cc_final: 0.8647 (m-90) REVERT: A 876 MET cc_start: 0.9781 (tpt) cc_final: 0.9404 (mtt) REVERT: A 1082 MET cc_start: 0.8784 (pmm) cc_final: 0.8446 (pmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0942 time to fit residues: 7.1371 Evaluate side-chains 39 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 HIS A 516 HIS ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.026680 restraints weight = 102767.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.027547 restraints weight = 69737.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.028138 restraints weight = 54715.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.028532 restraints weight = 46319.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.028758 restraints weight = 41620.351| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 11172 Z= 0.299 Angle : 1.064 38.121 15483 Z= 0.503 Chirality : 0.065 1.851 1739 Planarity : 0.006 0.058 1653 Dihedral : 24.320 177.607 2219 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 25.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.79 % Favored : 89.85 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.02 (0.25), residues: 1103 helix: 0.55 (0.21), residues: 550 sheet: -2.16 (0.54), residues: 75 loop : -1.91 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 469 TYR 0.018 0.003 TYR A 843 PHE 0.020 0.003 PHE A1109 TRP 0.012 0.002 TRP A 439 HIS 0.012 0.002 HIS A 349 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.30 (11156) covalent geometry : angle 1.04759 / 0.50 (15474) hydrogen bonds : bond 0.06867 / 4.82 ( 528) hydrogen bonds : angle 5.40043 / 3.90 ( 1483) metal coordination : bond 0.05006 / 2.01 ( 16) metal coordination : angle 7.87414 / 4.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6816 (mpp) cc_final: 0.6482 (mpp) REVERT: A 373 MET cc_start: 0.8736 (mmm) cc_final: 0.8502 (mmm) REVERT: A 483 LEU cc_start: 0.9831 (mt) cc_final: 0.9623 (mt) REVERT: A 569 MET cc_start: 0.9158 (mmp) cc_final: 0.8747 (mmm) REVERT: A 610 MET cc_start: 0.9610 (mmp) cc_final: 0.9197 (mmm) REVERT: A 876 MET cc_start: 0.9789 (tpt) cc_final: 0.9418 (mtt) REVERT: A 1082 MET cc_start: 0.8857 (pmm) cc_final: 0.8415 (pmm) REVERT: A 1103 ILE cc_start: 0.9780 (mt) cc_final: 0.9546 (mm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0943 time to fit residues: 7.1725 Evaluate side-chains 37 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.028339 restraints weight = 97066.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.029297 restraints weight = 64790.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.029956 restraints weight = 49910.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.030215 restraints weight = 41893.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030638 restraints weight = 38236.108| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 11172 Z= 0.152 Angle : 0.965 37.914 15483 Z= 0.444 Chirality : 0.063 1.881 1739 Planarity : 0.005 0.059 1653 Dihedral : 24.231 175.568 2219 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.43 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.65 (0.26), residues: 1103 helix: 0.91 (0.22), residues: 548 sheet: -2.50 (0.51), residues: 85 loop : -1.65 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 705 TYR 0.016 0.002 TYR A1024 PHE 0.011 0.002 PHE A 255 TRP 0.018 0.001 TRP A 822 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (11156) covalent geometry : angle 0.95086 / 0.44 (15474) hydrogen bonds : bond 0.04630 / 3.32 ( 528) hydrogen bonds : angle 5.05212 / 3.69 ( 1483) metal coordination : bond 0.04148 / 1.65 ( 16) metal coordination : angle 6.88380 / 3.78 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6868 (mpp) cc_final: 0.6597 (mpp) REVERT: A 373 MET cc_start: 0.8639 (mmm) cc_final: 0.8428 (mmm) REVERT: A 569 MET cc_start: 0.9114 (mmp) cc_final: 0.8644 (mmm) REVERT: A 610 MET cc_start: 0.9575 (mmp) cc_final: 0.9254 (mmm) REVERT: A 618 MET cc_start: 0.9725 (tpp) cc_final: 0.9438 (tpt) REVERT: A 756 TRP cc_start: 0.9051 (m-10) cc_final: 0.8711 (m-90) REVERT: A 876 MET cc_start: 0.9794 (tpt) cc_final: 0.9425 (mtt) REVERT: A 1082 MET cc_start: 0.8839 (pmm) cc_final: 0.8480 (pmm) REVERT: A 1103 ILE cc_start: 0.9755 (mt) cc_final: 0.9547 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0923 time to fit residues: 7.8406 Evaluate side-chains 41 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.027154 restraints weight = 98941.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.028062 restraints weight = 65873.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028623 restraints weight = 50733.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.029080 restraints weight = 43015.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.029281 restraints weight = 38506.224| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 11172 Z= 0.198 Angle : 0.979 38.045 15483 Z= 0.452 Chirality : 0.062 1.869 1739 Planarity : 0.005 0.060 1653 Dihedral : 24.123 175.533 2219 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.34 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.63 (0.26), residues: 1103 helix: 0.93 (0.22), residues: 550 sheet: -2.46 (0.52), residues: 82 loop : -1.66 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 168 TYR 0.012 0.002 TYR A 330 PHE 0.011 0.002 PHE A 403 TRP 0.011 0.002 TRP A 822 HIS 0.007 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (11156) covalent geometry : angle 0.96453 / 0.45 (15474) hydrogen bonds : bond 0.05243 / 3.69 ( 528) hydrogen bonds : angle 5.17817 / 3.78 ( 1483) metal coordination : bond 0.03609 / 1.46 ( 16) metal coordination : angle 7.06677 / 3.82 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.83 seconds wall clock time: 32 minutes 51.00 seconds (1971.00 seconds total)