Starting phenix.real_space_refine on Sat Aug 23 08:28:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl4_49517/08_2025/9nl4_49517.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl4_49517/08_2025/9nl4_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_2025/9nl4_49517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2025/9nl4_49517.map" model { file = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2025/9nl4_49517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl4_49517/08_2025/9nl4_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-2.0-5787/lib/python3.9/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: 2.45, 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: 1.22 Conformation dependent library (CDL) restraints added in 472.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.43 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: 2.80 Time building geometry restraints manager: 1.43 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=" CA PHE A 16 " pdb=" C PHE A 16 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.41e-02 5.03e+03 8.86e+00 bond pdb=" P DT B 45 " pdb=" O5' DT B 45 " ideal model delta sigma weight residual 1.600 1.658 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" P DT B 45 " pdb=" OP2 DT B 45 " ideal model delta sigma weight residual 1.480 1.535 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" CE LYS A 862 " pdb=" NZ LYS A 862 " ideal model delta sigma weight residual 1.489 1.570 -0.081 3.00e-02 1.11e+03 7.35e+00 bond pdb=" C ILE A 671 " pdb=" N GLN A 672 " ideal model delta sigma weight residual 1.327 1.293 0.033 1.71e-02 3.42e+03 3.82e+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 1.50e+00 4.44e-01 5.16e+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 - 0.458: 1729 0.458 - 0.916: 8 0.916 - 1.374: 0 1.374 - 1.832: 0 1.832 - 2.291: 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 2.35 0.05 2.29 2.00e-01 2.50e+01 1.31e+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 2.35 0.41 1.94 2.00e-01 2.50e+01 9.38e+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 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+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: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.008 0.491 11172 Z= 0.321 Angle : 1.139 40.869 15483 Z= 0.567 Chirality : 0.093 2.291 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 aren 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 covalent geometry : bond 0.00531 (11156) covalent geometry : angle 1.09485 (15474) hydrogen bonds : bond 0.18041 ( 528) hydrogen bonds : angle 7.73160 ( 1483) metal coordination : bond 0.16786 ( 16) metal coordination : angle 13.00655 ( 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 : 0.325 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: 0.1054 time to fit residues: 11.9738 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 : 0.320 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 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: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 349 HIS A 369 ASN A 544 HIS 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 = 0.3237 r_free = 0.3237 target = 0.049469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029822 restraints weight = 97308.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030766 restraints weight = 66559.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031365 restraints weight = 51598.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031870 restraints weight = 43656.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.032056 restraints weight = 38889.269| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11172 Z= 0.228 Angle : 0.993 41.126 15483 Z= 0.457 Chirality : 0.063 1.909 1739 Planarity : 0.006 0.070 1653 Dihedral : 24.707 175.833 2219 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.34 % Favored : 89.94 % Rotamer: Outliers : 0.20 % Allowed : 5.18 % Favored : 94.62 % 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 aren not related in a simple way. whole: -1.52 (0.26), residues: 1103 helix: 0.43 (0.22), residues: 538 sheet: -2.85 (0.54), residues: 75 loop : -2.40 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 469 TYR 0.014 0.002 TYR A 843 PHE 0.012 0.002 PHE A 357 TRP 0.018 0.002 TRP A 406 HIS 0.006 0.001 HIS A 734 Details of bonding type rmsd covalent geometry : bond 0.00474 (11156) covalent geometry : angle 0.97805 (15474) hydrogen bonds : bond 0.06525 ( 528) hydrogen bonds : angle 5.86402 ( 1483) metal coordination : bond 0.02079 ( 16) metal coordination : angle 7.08651 ( 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 : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9652 (mmp) cc_final: 0.9290 (ptm) REVERT: A 257 MET cc_start: 0.6754 (mpp) cc_final: 0.6310 (mpp) REVERT: A 373 MET cc_start: 0.8967 (mmp) cc_final: 0.8520 (mmm) REVERT: A 483 LEU cc_start: 0.9754 (mt) cc_final: 0.9493 (mt) REVERT: A 569 MET cc_start: 0.9233 (mmp) cc_final: 0.8793 (mmm) REVERT: A 618 MET cc_start: 0.9300 (tpp) cc_final: 0.8390 (tpp) REVERT: A 876 MET cc_start: 0.9691 (tpt) cc_final: 0.9362 (mtt) REVERT: A 975 MET cc_start: 0.9546 (mmp) cc_final: 0.9333 (mmm) REVERT: A 1078 THR cc_start: 0.9222 (t) cc_final: 0.9009 (p) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 0.0796 time to fit residues: 8.6484 Evaluate side-chains 44 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 154 HIS A 438 ASN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.049762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029954 restraints weight = 94035.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030963 restraints weight = 63854.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031645 restraints weight = 49278.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.032152 restraints weight = 41388.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032363 restraints weight = 36600.829| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 11172 Z= 0.174 Angle : 0.951 40.584 15483 Z= 0.432 Chirality : 0.062 1.904 1739 Planarity : 0.005 0.059 1653 Dihedral : 24.396 175.480 2219 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.62 % Favored : 91.66 % Rotamer: Outliers : 0.20 % Allowed : 3.45 % Favored : 96.35 % 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 aren not related in a simple way. whole: -0.84 (0.26), residues: 1103 helix: 0.99 (0.23), residues: 541 sheet: -2.49 (0.52), residues: 82 loop : -2.06 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 285 TYR 0.015 0.001 TYR A 330 PHE 0.023 0.001 PHE A 255 TRP 0.017 0.001 TRP A 406 HIS 0.007 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00360 (11156) covalent geometry : angle 0.93965 (15474) hydrogen bonds : bond 0.04749 ( 528) hydrogen bonds : angle 5.26211 ( 1483) metal coordination : bond 0.02861 ( 16) metal coordination : angle 6.20809 ( 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 66 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6959 (mpp) cc_final: 0.6298 (mpp) REVERT: A 373 MET cc_start: 0.8710 (mmp) cc_final: 0.8258 (mmm) REVERT: A 483 LEU cc_start: 0.9799 (mt) cc_final: 0.9588 (mt) REVERT: A 569 MET cc_start: 0.9112 (mmp) cc_final: 0.8612 (mmm) REVERT: A 610 MET cc_start: 0.8805 (tpt) cc_final: 0.8598 (tpt) REVERT: A 876 MET cc_start: 0.9732 (tpt) cc_final: 0.9349 (mtt) outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.0848 time to fit residues: 8.9510 Evaluate side-chains 48 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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: 0.9980 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 530 GLN ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.030117 restraints weight = 94120.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.031153 restraints weight = 63738.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031789 restraints weight = 48912.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.032327 restraints weight = 41280.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.032547 restraints weight = 36454.799| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11172 Z= 0.151 Angle : 0.944 41.073 15483 Z= 0.421 Chirality : 0.061 1.912 1739 Planarity : 0.005 0.053 1653 Dihedral : 24.308 174.843 2219 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.25 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 aren not related in a simple way. whole: -0.58 (0.26), residues: 1103 helix: 1.10 (0.22), residues: 538 sheet: -2.22 (0.52), residues: 82 loop : -1.80 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.015 0.001 TYR A 330 PHE 0.019 0.001 PHE A 628 TRP 0.012 0.001 TRP A 406 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00318 (11156) covalent geometry : angle 0.92352 (15474) hydrogen bonds : bond 0.04494 ( 528) hydrogen bonds : angle 5.03066 ( 1483) metal coordination : bond 0.02440 ( 16) metal coordination : angle 8.22934 ( 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 60 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9616 (mmp) cc_final: 0.9202 (ptm) REVERT: A 257 MET cc_start: 0.6920 (mpp) cc_final: 0.6511 (mpp) REVERT: A 569 MET cc_start: 0.9094 (mmp) cc_final: 0.8583 (mmm) REVERT: A 618 MET cc_start: 0.9398 (tpp) cc_final: 0.8319 (tpp) REVERT: A 876 MET cc_start: 0.9758 (tpt) cc_final: 0.9400 (mtt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0788 time to fit residues: 7.8528 Evaluate side-chains 45 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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: 9.9990 chunk 17 optimal weight: 0.0970 chunk 18 optimal weight: 0.0370 chunk 89 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 74 optimal weight: 0.0000 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** 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 = 0.3266 r_free = 0.3266 target = 0.050600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.030372 restraints weight = 92332.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031404 restraints weight = 62388.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032121 restraints weight = 48117.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032550 restraints weight = 40225.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032741 restraints weight = 35787.277| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 11172 Z= 0.143 Angle : 0.918 40.809 15483 Z= 0.407 Chirality : 0.060 1.922 1739 Planarity : 0.004 0.050 1653 Dihedral : 24.148 173.835 2219 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.25 % Favored : 92.20 % Rotamer: Outliers : 0.20 % Allowed : 2.44 % 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 aren not related in a simple way. whole: -0.57 (0.26), residues: 1103 helix: 1.05 (0.22), residues: 547 sheet: -2.16 (0.52), residues: 82 loop : -1.79 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.013 0.001 TYR A 330 PHE 0.013 0.001 PHE A 628 TRP 0.010 0.001 TRP A 822 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00299 (11156) covalent geometry : angle 0.90514 (15474) hydrogen bonds : bond 0.04166 ( 528) hydrogen bonds : angle 4.85689 ( 1483) metal coordination : bond 0.03406 ( 16) metal coordination : angle 6.37803 ( 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 66 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.9623 (mmp) cc_final: 0.9167 (ptm) REVERT: A 257 MET cc_start: 0.6875 (mpp) cc_final: 0.6468 (mpp) REVERT: A 373 MET cc_start: 0.8370 (mmp) cc_final: 0.7774 (mmm) REVERT: A 569 MET cc_start: 0.9062 (mmp) cc_final: 0.8507 (mmm) REVERT: A 618 MET cc_start: 0.9402 (tpp) cc_final: 0.8458 (tpp) REVERT: A 756 TRP cc_start: 0.8809 (m-10) cc_final: 0.8524 (m-90) REVERT: A 876 MET cc_start: 0.9756 (tpt) cc_final: 0.9383 (mtt) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.0801 time to fit residues: 8.8256 Evaluate side-chains 47 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 74 optimal weight: 0.0870 chunk 80 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 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 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.028063 restraints weight = 97627.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.028989 restraints weight = 66669.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.029564 restraints weight = 51873.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.029848 restraints weight = 44114.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030272 restraints weight = 40134.712| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 11172 Z= 0.234 Angle : 0.973 41.254 15483 Z= 0.442 Chirality : 0.061 1.892 1739 Planarity : 0.005 0.054 1653 Dihedral : 24.120 174.981 2219 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.07 % Favored : 91.48 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 aren not related in a simple way. whole: -0.57 (0.26), residues: 1103 helix: 0.99 (0.22), residues: 550 sheet: -2.36 (0.52), residues: 84 loop : -1.67 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 469 TYR 0.014 0.002 TYR A 330 PHE 0.014 0.002 PHE A 628 TRP 0.012 0.002 TRP A 334 HIS 0.009 0.002 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00485 (11156) covalent geometry : angle 0.95380 (15474) hydrogen bonds : bond 0.05307 ( 528) hydrogen bonds : angle 5.12335 ( 1483) metal coordination : bond 0.03145 ( 16) metal coordination : angle 7.96323 ( 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 50 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.360 Fit side-chains REVERT: A 210 MET cc_start: 0.8888 (ptp) cc_final: 0.8606 (ptp) REVERT: A 257 MET cc_start: 0.6708 (mpp) cc_final: 0.6376 (mpp) REVERT: A 373 MET cc_start: 0.8901 (mmp) cc_final: 0.8453 (mmm) REVERT: A 569 MET cc_start: 0.9107 (mmp) cc_final: 0.8674 (mmm) REVERT: A 756 TRP cc_start: 0.8966 (m-10) cc_final: 0.8661 (m-90) REVERT: A 876 MET cc_start: 0.9778 (tpt) cc_final: 0.9412 (mtt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0759 time to fit residues: 6.3688 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 : 0.393 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 0.0040 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 97 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 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 116 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 = 0.3239 r_free = 0.3239 target = 0.049549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.029267 restraints weight = 92570.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.030283 restraints weight = 62145.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030996 restraints weight = 47565.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031459 restraints weight = 39701.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.031684 restraints weight = 35385.580| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 11172 Z= 0.141 Angle : 0.922 40.683 15483 Z= 0.408 Chirality : 0.061 1.933 1739 Planarity : 0.004 0.056 1653 Dihedral : 24.004 173.638 2219 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.25 % Favored : 92.29 % Rotamer: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.97 % 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 aren not related in a simple way. whole: -0.44 (0.26), residues: 1103 helix: 1.08 (0.22), residues: 553 sheet: -2.34 (0.51), residues: 85 loop : -1.58 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.014 0.001 TYR A 330 PHE 0.015 0.001 PHE A 255 TRP 0.014 0.001 TRP A 822 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00297 (11156) covalent geometry : angle 0.90662 (15474) hydrogen bonds : bond 0.03990 ( 528) hydrogen bonds : angle 4.80508 ( 1483) metal coordination : bond 0.04282 ( 16) metal coordination : angle 7.07707 ( 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 55 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 MET cc_start: 0.8917 (mmp) cc_final: 0.8444 (mmm) REVERT: A 569 MET cc_start: 0.9133 (mmp) cc_final: 0.8667 (mmm) REVERT: A 610 MET cc_start: 0.9438 (mmp) cc_final: 0.9002 (mmm) REVERT: A 618 MET cc_start: 0.9550 (tpp) cc_final: 0.9326 (tpp) REVERT: A 756 TRP cc_start: 0.8893 (m-10) cc_final: 0.8532 (m-90) REVERT: A 876 MET cc_start: 0.9789 (tpt) cc_final: 0.9378 (mtt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.0820 time to fit residues: 7.3670 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 : 0.391 ------------------------------------------------------------------------------- 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: 5.9990 chunk 38 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 3 optimal weight: 40.0000 chunk 115 optimal weight: 7.9990 chunk 17 optimal weight: 0.0670 chunk 67 optimal weight: 4.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 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 118 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.046771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.027354 restraints weight = 98306.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.028277 restraints weight = 66270.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.028868 restraints weight = 51140.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.029315 restraints weight = 43221.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029481 restraints weight = 38455.399| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 11172 Z= 0.247 Angle : 0.960 41.034 15483 Z= 0.438 Chirality : 0.061 1.885 1739 Planarity : 0.005 0.055 1653 Dihedral : 23.953 175.231 2219 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.71 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 aren not related in a simple way. whole: -0.47 (0.26), residues: 1103 helix: 0.96 (0.22), residues: 551 sheet: -1.98 (0.55), residues: 79 loop : -1.56 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 469 TYR 0.022 0.002 TYR A1040 PHE 0.013 0.002 PHE A 85 TRP 0.011 0.002 TRP A 822 HIS 0.008 0.002 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00514 (11156) covalent geometry : angle 0.94670 (15474) hydrogen bonds : bond 0.05091 ( 528) hydrogen bonds : angle 5.11100 ( 1483) metal coordination : bond 0.02841 ( 16) metal coordination : angle 6.76936 ( 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 51 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.6751 (mpp) cc_final: 0.6491 (mpp) REVERT: A 373 MET cc_start: 0.8960 (mmp) cc_final: 0.8603 (mmm) REVERT: A 569 MET cc_start: 0.9191 (mmp) cc_final: 0.8786 (mmm) REVERT: A 610 MET cc_start: 0.9463 (mmp) cc_final: 0.9003 (mmm) REVERT: A 618 MET cc_start: 0.9472 (tpp) cc_final: 0.9171 (tpp) REVERT: A 756 TRP cc_start: 0.9037 (m-10) cc_final: 0.8601 (m-90) REVERT: A 876 MET cc_start: 0.9793 (tpt) cc_final: 0.9402 (mtt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0826 time to fit residues: 6.8327 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 : 0.391 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** 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 = 0.3184 r_free = 0.3184 target = 0.047516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.027583 restraints weight = 95726.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.028554 restraints weight = 64100.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.029118 restraints weight = 49120.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.029577 restraints weight = 41639.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.029866 restraints weight = 37274.630| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 11172 Z= 0.161 Angle : 0.924 41.130 15483 Z= 0.413 Chirality : 0.061 1.920 1739 Planarity : 0.005 0.056 1653 Dihedral : 23.876 174.330 2219 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.34 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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 aren not related in a simple way. whole: -0.36 (0.26), residues: 1103 helix: 1.03 (0.22), residues: 552 sheet: -1.94 (0.54), residues: 79 loop : -1.47 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.014 0.001 TYR A 330 PHE 0.013 0.001 PHE A1094 TRP 0.013 0.001 TRP A 822 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00340 (11156) covalent geometry : angle 0.91160 (15474) hydrogen bonds : bond 0.04147 ( 528) hydrogen bonds : angle 4.95603 ( 1483) metal coordination : bond 0.03348 ( 16) metal coordination : angle 6.35176 ( 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 50 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.6892 (mpp) cc_final: 0.6562 (mpp) REVERT: A 373 MET cc_start: 0.8919 (mmp) cc_final: 0.8510 (mmm) REVERT: A 569 MET cc_start: 0.9169 (mmp) cc_final: 0.8760 (mmm) REVERT: A 610 MET cc_start: 0.9541 (mmp) cc_final: 0.9062 (mmm) REVERT: A 618 MET cc_start: 0.9477 (tpp) cc_final: 0.9240 (tpp) REVERT: A 756 TRP cc_start: 0.8970 (m-10) cc_final: 0.8546 (m-90) REVERT: A 876 MET cc_start: 0.9792 (tpt) cc_final: 0.9440 (mtt) REVERT: A 1103 ILE cc_start: 0.9683 (mm) cc_final: 0.9480 (mm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0980 time to fit residues: 7.7149 Evaluate side-chains 43 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 6.9990 chunk 66 optimal weight: 0.0170 chunk 68 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.046714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.027015 restraints weight = 97112.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.027918 restraints weight = 65095.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.028497 restraints weight = 50172.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.028852 restraints weight = 42554.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.029202 restraints weight = 38256.206| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11172 Z= 0.181 Angle : 0.937 41.422 15483 Z= 0.419 Chirality : 0.061 1.902 1739 Planarity : 0.005 0.058 1653 Dihedral : 23.788 174.153 2219 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.52 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 aren not related in a simple way. whole: -0.36 (0.26), residues: 1103 helix: 0.96 (0.22), residues: 554 sheet: -1.68 (0.60), residues: 69 loop : -1.45 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 168 TYR 0.012 0.002 TYR A 330 PHE 0.015 0.002 PHE A 913 TRP 0.011 0.002 TRP A 76 HIS 0.007 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00384 (11156) covalent geometry : angle 0.92455 (15474) hydrogen bonds : bond 0.04474 ( 528) hydrogen bonds : angle 4.98394 ( 1483) metal coordination : bond 0.02839 ( 16) metal coordination : angle 6.37371 ( 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 48 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 257 MET cc_start: 0.7084 (mpp) cc_final: 0.6812 (mpp) REVERT: A 373 MET cc_start: 0.8897 (mmp) cc_final: 0.8564 (mmm) REVERT: A 569 MET cc_start: 0.9199 (mmp) cc_final: 0.8809 (mmm) REVERT: A 610 MET cc_start: 0.9564 (mmp) cc_final: 0.9138 (mmm) REVERT: A 756 TRP cc_start: 0.9056 (m-10) cc_final: 0.8644 (m-90) REVERT: A 876 MET cc_start: 0.9801 (tpt) cc_final: 0.9427 (mtt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0882 time to fit residues: 6.9280 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 : 0.383 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** 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 = 0.3176 r_free = 0.3176 target = 0.046984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.027260 restraints weight = 96793.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.028170 restraints weight = 64108.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.028728 restraints weight = 49583.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029005 restraints weight = 41870.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029415 restraints weight = 38022.609| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.725 11172 Z= 0.331 Angle : 0.936 41.314 15483 Z= 0.414 Chirality : 0.061 1.917 1739 Planarity : 0.005 0.059 1653 Dihedral : 23.777 173.895 2219 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.43 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 aren not related in a simple way. whole: -0.34 (0.26), residues: 1103 helix: 1.02 (0.22), residues: 554 sheet: -1.99 (0.56), residues: 74 loop : -1.44 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 168 TYR 0.014 0.002 TYR A 540 PHE 0.012 0.001 PHE A1094 TRP 0.012 0.001 TRP A 822 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00334 (11156) covalent geometry : angle 0.91266 (15474) hydrogen bonds : bond 0.04059 ( 528) hydrogen bonds : angle 4.87493 ( 1483) metal coordination : bond 0.43209 ( 16) metal coordination : angle 8.74115 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.50 seconds wall clock time: 33 minutes 9.18 seconds (1989.18 seconds total)