Starting phenix.real_space_refine on Sat Aug 23 11:16:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwe_18693/08_2025/8qwe_18693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwe_18693/08_2025/8qwe_18693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qwe_18693/08_2025/8qwe_18693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwe_18693/08_2025/8qwe_18693.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qwe_18693/08_2025/8qwe_18693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwe_18693/08_2025/8qwe_18693.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 88 5.49 5 Mg 5 5.21 5 S 18 5.16 5 C 7169 2.51 5 N 1954 2.21 5 O 2487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11721 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9886 Classifications: {'peptide': 1185} Link IDs: {'PTRANS': 30, 'TRANS': 1154} Chain breaks: 6 Chain: "C" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 717 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 13} Link IDs: {'rna2p': 10, 'rna3p': 23} Chain breaks: 1 Chain: "T" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 603 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 510 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.05, per 1000 atoms: 0.26 Number of scatterers: 11721 At special positions: 0 Unit cell: (101.327, 96.3846, 141.694, 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) S 18 16.00 P 88 15.00 Mg 5 11.99 O 2487 8.00 N 1954 7.00 C 7169 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: 1.18 Conformation dependent library (CDL) restraints added in 559.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 49.1% alpha, 8.2% beta 24 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 Processing helix chain 'A' and resid 36 through 67 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.536A pdb=" N GLU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 117 removed outlier: 4.047A pdb=" N GLU A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N HIS A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 3.698A pdb=" N LEU A 123 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 4.160A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.756A pdb=" N PHE A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.834A pdb=" N ASN A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 Processing helix chain 'A' and resid 188 through 207 removed outlier: 3.661A pdb=" N LYS A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N HIS A 207 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 245 through 257 Processing helix chain 'A' and resid 270 through 283 removed outlier: 3.808A pdb=" N TYR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 315 through 331 removed outlier: 3.507A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.958A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 removed outlier: 4.023A pdb=" N THR A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.759A pdb=" N SER A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 Processing helix chain 'A' and resid 491 through 510 removed outlier: 3.529A pdb=" N ILE A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 542 removed outlier: 4.447A pdb=" N GLU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 604 through 607 removed outlier: 3.780A pdb=" N ASN A 607 " --> pdb=" O LYS A 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 633 through 643 Proline residue: A 639 - end of helix Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 674 through 692 Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.812A pdb=" N GLY A 699 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.631A pdb=" N TYR A 708 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 722 removed outlier: 3.996A pdb=" N PHE A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 751 through 755 Processing helix chain 'A' and resid 763 through 773 removed outlier: 4.123A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 780 removed outlier: 3.766A pdb=" N ASP A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 857 through 866 Processing helix chain 'A' and resid 913 through 931 Processing helix chain 'A' and resid 938 through 961 removed outlier: 3.506A pdb=" N LEU A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 948 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 removed outlier: 4.054A pdb=" N TYR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1072 removed outlier: 3.910A pdb=" N LYS A1067 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1140 Processing helix chain 'A' and resid 1141 through 1143 No H-bonds generated for 'chain 'A' and resid 1141 through 1143' Processing helix chain 'A' and resid 1152 through 1156 removed outlier: 3.962A pdb=" N ILE A1156 " --> pdb=" O LYS A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1173 Processing helix chain 'A' and resid 1216 through 1237 removed outlier: 4.076A pdb=" N ALA A1220 " --> pdb=" O ASP A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1257 Processing sheet with id=AA1, first strand: chain 'A' and resid 589 through 593 removed outlier: 4.777A pdb=" N TYR A 597 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 363 Processing sheet with id=AA3, first strand: chain 'A' and resid 564 through 566 Processing sheet with id=AA4, first strand: chain 'A' and resid 622 through 630 Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 810 through 811 Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 901 removed outlier: 6.732A pdb=" N LEU A 889 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN A 899 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU A 887 " --> pdb=" O GLN A 899 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN A 873 " --> pdb=" O ILE A 963 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL A 965 " --> pdb=" O ASN A 873 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE A 875 " --> pdb=" O VAL A 965 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLU A 967 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ILE A 877 " --> pdb=" O GLU A 967 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1075 through 1078 Processing sheet with id=AA9, first strand: chain 'A' and resid 1112 through 1113 Processing sheet with id=AB1, first strand: chain 'A' and resid 1180 through 1181 removed outlier: 3.794A pdb=" N TYR A1189 " --> pdb=" O ASN A1180 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.15: 1 1.15 - 1.32: 1889 1.32 - 1.48: 5109 1.48 - 1.64: 5107 1.64 - 1.81: 32 Bond restraints: 12138 Sorted by residual: bond pdb=" CG PRO A 815 " pdb=" CD PRO A 815 " ideal model delta sigma weight residual 1.503 0.988 0.515 3.40e-02 8.65e+02 2.30e+02 bond pdb=" N PRO A 815 " pdb=" CA PRO A 815 " ideal model delta sigma weight residual 1.469 1.508 -0.039 1.28e-02 6.10e+03 9.39e+00 bond pdb=" N PRO A 815 " pdb=" CD PRO A 815 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.22e+00 bond pdb=" CA PRO A 815 " pdb=" CB PRO A 815 " ideal model delta sigma weight residual 1.533 1.498 0.035 1.42e-02 4.96e+03 6.06e+00 bond pdb=" C ALA A 869 " pdb=" N PRO A 870 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.68e+00 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 16708 6.18 - 12.37: 9 12.37 - 18.55: 0 18.55 - 24.74: 0 24.74 - 30.92: 2 Bond angle restraints: 16719 Sorted by residual: angle pdb=" N PRO A 815 " pdb=" CD PRO A 815 " pdb=" CG PRO A 815 " ideal model delta sigma weight residual 103.20 72.28 30.92 1.50e+00 4.44e-01 4.25e+02 angle pdb=" CA PRO A 815 " pdb=" CB PRO A 815 " pdb=" CG PRO A 815 " ideal model delta sigma weight residual 104.50 73.63 30.87 1.90e+00 2.77e-01 2.64e+02 angle pdb=" N PRO A 815 " pdb=" CA PRO A 815 " pdb=" CB PRO A 815 " ideal model delta sigma weight residual 103.25 92.70 10.55 1.05e+00 9.07e-01 1.01e+02 angle pdb=" CA PRO A 815 " pdb=" N PRO A 815 " pdb=" CD PRO A 815 " ideal model delta sigma weight residual 112.00 105.52 6.48 1.40e+00 5.10e-01 2.14e+01 angle pdb=" C ASP A1119 " pdb=" CA ASP A1119 " pdb=" CB ASP A1119 " ideal model delta sigma weight residual 116.34 109.87 6.47 1.40e+00 5.10e-01 2.14e+01 ... (remaining 16714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 6757 35.44 - 70.87: 474 70.87 - 106.31: 22 106.31 - 141.74: 0 141.74 - 177.18: 2 Dihedral angle restraints: 7255 sinusoidal: 3741 harmonic: 3514 Sorted by residual: dihedral pdb=" N PRO A 815 " pdb=" CG PRO A 815 " pdb=" CD PRO A 815 " pdb=" CB PRO A 815 " ideal model delta sinusoidal sigma weight residual -30.00 -84.48 54.48 1 1.50e+01 4.44e-03 1.79e+01 dihedral pdb=" CA PHE A 971 " pdb=" C PHE A 971 " pdb=" N GLY A 972 " pdb=" CA GLY A 972 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PRO A 815 " pdb=" CB PRO A 815 " pdb=" CG PRO A 815 " pdb=" CD PRO A 815 " ideal model delta sinusoidal sigma weight residual -38.00 -108.96 70.96 1 2.00e+01 2.50e-03 1.62e+01 ... (remaining 7252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1203 0.029 - 0.058: 422 0.058 - 0.087: 101 0.087 - 0.116: 61 0.116 - 0.145: 12 Chirality restraints: 1799 Sorted by residual: chirality pdb=" C1' U C -15 " pdb=" O4' U C -15 " pdb=" C2' U C -15 " pdb=" N1 U C -15 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.14 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA ILE A 802 " pdb=" N ILE A 802 " pdb=" C ILE A 802 " pdb=" CB ILE A 802 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA LEU A 414 " pdb=" N LEU A 414 " pdb=" C LEU A 414 " pdb=" CB LEU A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1796 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 289 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 290 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 128 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C LEU A 128 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 128 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 129 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1047 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A1048 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1048 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1048 " 0.026 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 98 2.60 - 3.18: 9600 3.18 - 3.75: 18709 3.75 - 4.33: 25603 4.33 - 4.90: 40967 Nonbonded interactions: 94977 Sorted by model distance: nonbonded pdb=" NZ LYS A 974 " pdb="MG MG A1404 " model vdw 2.028 2.250 nonbonded pdb=" OD1 ASP A 878 " pdb="MG MG A1404 " model vdw 2.052 2.170 nonbonded pdb=" O ARG A 552 " pdb=" OG1 THR A 556 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR A 12 " pdb=" O THR A1019 " model vdw 2.214 3.040 nonbonded pdb=" OG1 THR A 159 " pdb=" OP2 DT N -3 " model vdw 2.217 3.040 ... (remaining 94972 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.720 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.005 0.515 12138 Z= 0.184 Angle : 0.599 30.924 16719 Z= 0.341 Chirality : 0.036 0.145 1799 Planarity : 0.003 0.048 1850 Dihedral : 20.601 177.176 4981 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.25), residues: 1171 helix: 1.26 (0.24), residues: 504 sheet: -1.24 (0.48), residues: 128 loop : -1.80 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 925 TYR 0.016 0.001 TYR A 278 PHE 0.010 0.001 PHE A1135 TRP 0.005 0.001 TRP A1252 HIS 0.003 0.000 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00532 (12138) covalent geometry : angle 0.59946 (16719) hydrogen bonds : bond 0.15806 ( 469) hydrogen bonds : angle 6.12861 ( 1282) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.411 Fit side-chains REVERT: A 108 LYS cc_start: 0.7577 (tmtt) cc_final: 0.6772 (mtmt) REVERT: A 660 ILE cc_start: 0.8394 (mm) cc_final: 0.8152 (mm) REVERT: A 1090 ASP cc_start: 0.8263 (t0) cc_final: 0.7248 (p0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1478 time to fit residues: 16.5127 Evaluate side-chains 68 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128806 restraints weight = 14782.937| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.31 r_work: 0.3348 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12138 Z= 0.130 Angle : 0.513 8.771 16719 Z= 0.279 Chirality : 0.038 0.151 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.674 177.181 2387 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.11 % Allowed : 23.67 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.25), residues: 1171 helix: 1.35 (0.23), residues: 513 sheet: -1.08 (0.49), residues: 126 loop : -1.66 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1173 TYR 0.016 0.001 TYR A 628 PHE 0.010 0.001 PHE A1087 TRP 0.006 0.001 TRP A1252 HIS 0.003 0.000 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00280 (12138) covalent geometry : angle 0.51338 (16719) hydrogen bonds : bond 0.03876 ( 469) hydrogen bonds : angle 4.58698 ( 1282) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.414 Fit side-chains REVERT: A 272 ASN cc_start: 0.4937 (OUTLIER) cc_final: 0.4572 (p0) REVERT: A 1090 ASP cc_start: 0.8384 (t0) cc_final: 0.7541 (p0) outliers start: 23 outliers final: 13 residues processed: 91 average time/residue: 0.1203 time to fit residues: 15.6085 Evaluate side-chains 82 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.202623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126895 restraints weight = 14868.547| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.49 r_work: 0.3275 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12138 Z= 0.215 Angle : 0.568 8.179 16719 Z= 0.306 Chirality : 0.041 0.197 1799 Planarity : 0.003 0.051 1850 Dihedral : 19.874 178.402 2387 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.39 % Allowed : 23.03 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.25), residues: 1171 helix: 1.22 (0.23), residues: 508 sheet: -1.03 (0.48), residues: 128 loop : -1.62 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.029 0.002 TYR A 628 PHE 0.014 0.001 PHE A 8 TRP 0.007 0.001 TRP A1252 HIS 0.004 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00502 (12138) covalent geometry : angle 0.56826 (16719) hydrogen bonds : bond 0.04192 ( 469) hydrogen bonds : angle 4.59508 ( 1282) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7889 (ttm-80) REVERT: A 108 LYS cc_start: 0.7526 (tmtt) cc_final: 0.6760 (mtmt) REVERT: A 272 ASN cc_start: 0.4976 (OUTLIER) cc_final: 0.4598 (p0) REVERT: A 414 LEU cc_start: -0.2029 (OUTLIER) cc_final: -0.2871 (mp) REVERT: A 882 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7666 (mmt-90) REVERT: A 1090 ASP cc_start: 0.8354 (t0) cc_final: 0.7464 (p0) REVERT: A 1091 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: A 1177 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6791 (pp30) outliers start: 37 outliers final: 20 residues processed: 109 average time/residue: 0.1149 time to fit residues: 17.7450 Evaluate side-chains 96 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 ARG Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1177 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.203438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.128251 restraints weight = 14814.263| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.74 r_work: 0.3307 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12138 Z= 0.168 Angle : 0.536 8.218 16719 Z= 0.289 Chirality : 0.039 0.185 1799 Planarity : 0.003 0.050 1850 Dihedral : 19.854 178.387 2387 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.30 % Allowed : 22.84 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1171 helix: 1.23 (0.23), residues: 509 sheet: -1.04 (0.47), residues: 128 loop : -1.62 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.025 0.001 TYR A 628 PHE 0.013 0.001 PHE A1135 TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00385 (12138) covalent geometry : angle 0.53584 (16719) hydrogen bonds : bond 0.03803 ( 469) hydrogen bonds : angle 4.43189 ( 1282) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 74 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7394 (tmtt) cc_final: 0.6647 (mtmt) REVERT: A 272 ASN cc_start: 0.4688 (OUTLIER) cc_final: 0.4358 (p0) REVERT: A 1090 ASP cc_start: 0.8255 (t0) cc_final: 0.7410 (p0) REVERT: A 1091 TYR cc_start: 0.7395 (OUTLIER) cc_final: 0.6685 (m-10) outliers start: 36 outliers final: 22 residues processed: 102 average time/residue: 0.1083 time to fit residues: 15.7608 Evaluate side-chains 95 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 41 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.202243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123932 restraints weight = 14757.247| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.17 r_work: 0.3332 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12138 Z= 0.207 Angle : 0.562 8.087 16719 Z= 0.302 Chirality : 0.041 0.198 1799 Planarity : 0.003 0.051 1850 Dihedral : 19.920 178.808 2387 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.21 % Allowed : 22.66 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.25), residues: 1171 helix: 1.24 (0.23), residues: 502 sheet: -1.05 (0.47), residues: 128 loop : -1.54 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1111 TYR 0.028 0.001 TYR A 628 PHE 0.013 0.001 PHE A 8 TRP 0.008 0.001 TRP A1124 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00484 (12138) covalent geometry : angle 0.56191 (16719) hydrogen bonds : bond 0.03937 ( 469) hydrogen bonds : angle 4.47854 ( 1282) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7535 (tmtt) cc_final: 0.6774 (mtmt) REVERT: A 272 ASN cc_start: 0.4838 (OUTLIER) cc_final: 0.4451 (p0) REVERT: A 826 TYR cc_start: 0.9008 (p90) cc_final: 0.8786 (p90) REVERT: A 1090 ASP cc_start: 0.8327 (t0) cc_final: 0.7438 (p0) REVERT: A 1091 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6584 (m-10) outliers start: 35 outliers final: 25 residues processed: 101 average time/residue: 0.0858 time to fit residues: 12.8667 Evaluate side-chains 96 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 118 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.203414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125085 restraints weight = 14741.907| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.17 r_work: 0.3316 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12138 Z= 0.157 Angle : 0.542 12.245 16719 Z= 0.290 Chirality : 0.039 0.184 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.893 178.593 2387 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.58 % Allowed : 22.29 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.25), residues: 1171 helix: 1.34 (0.23), residues: 502 sheet: -1.02 (0.47), residues: 128 loop : -1.51 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1173 TYR 0.023 0.001 TYR A 628 PHE 0.031 0.001 PHE A1135 TRP 0.007 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00360 (12138) covalent geometry : angle 0.54237 (16719) hydrogen bonds : bond 0.03645 ( 469) hydrogen bonds : angle 4.37929 ( 1282) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 73 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7494 (tmtt) cc_final: 0.6725 (mtmt) REVERT: A 272 ASN cc_start: 0.4727 (OUTLIER) cc_final: 0.4358 (p0) REVERT: A 668 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7364 (mtmt) REVERT: A 1090 ASP cc_start: 0.8315 (t0) cc_final: 0.7433 (p0) REVERT: A 1091 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6534 (m-10) outliers start: 39 outliers final: 27 residues processed: 105 average time/residue: 0.0960 time to fit residues: 14.7659 Evaluate side-chains 98 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1115 TYR Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.200091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128457 restraints weight = 14711.705| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.53 r_work: 0.3288 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12138 Z= 0.285 Angle : 0.632 11.928 16719 Z= 0.334 Chirality : 0.044 0.226 1799 Planarity : 0.004 0.054 1850 Dihedral : 20.058 179.957 2387 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.67 % Allowed : 22.11 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.25), residues: 1171 helix: 1.13 (0.23), residues: 502 sheet: -1.09 (0.47), residues: 128 loop : -1.63 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 833 TYR 0.032 0.002 TYR A 628 PHE 0.028 0.002 PHE A1135 TRP 0.018 0.002 TRP A1124 HIS 0.006 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00670 (12138) covalent geometry : angle 0.63238 (16719) hydrogen bonds : bond 0.04413 ( 469) hydrogen bonds : angle 4.61789 ( 1282) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7482 (tmtt) cc_final: 0.6713 (mtmt) REVERT: A 1090 ASP cc_start: 0.8325 (t0) cc_final: 0.7483 (p0) REVERT: A 1091 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6500 (m-10) outliers start: 40 outliers final: 32 residues processed: 101 average time/residue: 0.1120 time to fit residues: 16.2707 Evaluate side-chains 100 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 TYR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.202001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.126198 restraints weight = 14745.044| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.63 r_work: 0.3269 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12138 Z= 0.185 Angle : 0.567 11.613 16719 Z= 0.302 Chirality : 0.041 0.194 1799 Planarity : 0.003 0.052 1850 Dihedral : 19.951 179.330 2387 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.12 % Allowed : 22.48 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1171 helix: 1.26 (0.23), residues: 500 sheet: -1.11 (0.46), residues: 131 loop : -1.59 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1173 TYR 0.026 0.001 TYR A 628 PHE 0.025 0.001 PHE A1135 TRP 0.016 0.001 TRP A1124 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00430 (12138) covalent geometry : angle 0.56695 (16719) hydrogen bonds : bond 0.03816 ( 469) hydrogen bonds : angle 4.44211 ( 1282) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7823 (ttm-80) REVERT: A 108 LYS cc_start: 0.7398 (tmtt) cc_final: 0.6628 (mtmt) REVERT: A 668 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7385 (mtmt) REVERT: A 826 TYR cc_start: 0.8941 (p90) cc_final: 0.8741 (p90) REVERT: A 1090 ASP cc_start: 0.8258 (t0) cc_final: 0.7415 (p0) REVERT: A 1091 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6502 (m-10) outliers start: 34 outliers final: 27 residues processed: 97 average time/residue: 0.1097 time to fit residues: 15.7736 Evaluate side-chains 94 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 668 LYS Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 TYR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 951 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.205369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131290 restraints weight = 14609.248| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.64 r_work: 0.3310 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12138 Z= 0.125 Angle : 0.530 11.413 16719 Z= 0.282 Chirality : 0.038 0.167 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.793 177.870 2387 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.39 % Allowed : 23.30 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.25), residues: 1171 helix: 1.36 (0.23), residues: 508 sheet: -1.03 (0.46), residues: 131 loop : -1.57 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1173 TYR 0.020 0.001 TYR A 628 PHE 0.024 0.001 PHE A1135 TRP 0.014 0.001 TRP A1124 HIS 0.004 0.000 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00275 (12138) covalent geometry : angle 0.52951 (16719) hydrogen bonds : bond 0.03321 ( 469) hydrogen bonds : angle 4.26703 ( 1282) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7362 (tmtt) cc_final: 0.6606 (mtmt) REVERT: A 826 TYR cc_start: 0.8914 (p90) cc_final: 0.8710 (p90) REVERT: A 920 ASP cc_start: 0.7254 (m-30) cc_final: 0.7045 (m-30) REVERT: A 1023 GLU cc_start: 0.7744 (mp0) cc_final: 0.7384 (mp0) REVERT: A 1090 ASP cc_start: 0.8191 (t0) cc_final: 0.7391 (p0) REVERT: A 1091 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6624 (m-10) outliers start: 26 outliers final: 23 residues processed: 94 average time/residue: 0.1093 time to fit residues: 15.2948 Evaluate side-chains 93 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 TYR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 36 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.204408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130094 restraints weight = 14867.414| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.75 r_work: 0.3283 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12138 Z= 0.151 Angle : 0.549 11.105 16719 Z= 0.292 Chirality : 0.039 0.180 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.804 178.192 2387 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.57 % Allowed : 23.49 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.25), residues: 1171 helix: 1.35 (0.23), residues: 506 sheet: -1.16 (0.46), residues: 131 loop : -1.55 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1173 TYR 0.023 0.001 TYR A 628 PHE 0.024 0.001 PHE A1135 TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00347 (12138) covalent geometry : angle 0.54884 (16719) hydrogen bonds : bond 0.03487 ( 469) hydrogen bonds : angle 4.31512 ( 1282) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7396 (tmtt) cc_final: 0.6639 (mtmt) REVERT: A 826 TYR cc_start: 0.8923 (p90) cc_final: 0.8686 (p90) REVERT: A 1090 ASP cc_start: 0.8214 (t0) cc_final: 0.7449 (p0) REVERT: A 1091 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: A 1173 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6474 (mtm-85) outliers start: 28 outliers final: 23 residues processed: 92 average time/residue: 0.1137 time to fit residues: 15.5006 Evaluate side-chains 92 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 909 HIS Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 938 ILE Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 973 PHE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1001 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1053 VAL Chi-restraints excluded: chain A residue 1091 TYR Chi-restraints excluded: chain A residue 1094 PHE Chi-restraints excluded: chain A residue 1115 TYR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 50.0000 chunk 94 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 30.0000 chunk 30 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.201439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122682 restraints weight = 14756.506| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.14 r_work: 0.3284 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12138 Z= 0.215 Angle : 0.597 10.862 16719 Z= 0.317 Chirality : 0.042 0.211 1799 Planarity : 0.003 0.051 1850 Dihedral : 19.954 179.347 2387 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.94 % Allowed : 23.21 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.25), residues: 1171 helix: 1.26 (0.23), residues: 501 sheet: -1.16 (0.46), residues: 131 loop : -1.56 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1173 TYR 0.027 0.002 TYR A 628 PHE 0.022 0.001 PHE A1135 TRP 0.012 0.001 TRP A1124 HIS 0.005 0.001 HIS A1222 Details of bonding type rmsd covalent geometry : bond 0.00505 (12138) covalent geometry : angle 0.59739 (16719) hydrogen bonds : bond 0.03977 ( 469) hydrogen bonds : angle 4.52459 ( 1282) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.50 seconds wall clock time: 59 minutes 22.44 seconds (3562.44 seconds total)