Starting phenix.real_space_refine on Wed May 14 10:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qwe_18693/05_2025/8qwe_18693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qwe_18693/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qwe_18693/05_2025/8qwe_18693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qwe_18693/05_2025/8qwe_18693.map" model { file = "/net/cci-nas-00/data/ceres_data/8qwe_18693/05_2025/8qwe_18693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qwe_18693/05_2025/8qwe_18693.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.42, per 1000 atoms: 0.63 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: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.92 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: 5.02 Time building geometry restraints manager: 3.37 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: 1.580 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: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 32.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP A1252 HIS 0.003 0.000 HIS A1222 PHE 0.010 0.001 PHE A1135 TYR 0.016 0.001 TYR A 278 ARG 0.001 0.000 ARG A 925 Details of bonding type rmsd hydrogen bonds : bond 0.15806 ( 469) hydrogen bonds : angle 6.12861 ( 1282) covalent geometry : bond 0.00532 (12138) covalent geometry : angle 0.59946 (16719) *********************** 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 : 1.212 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: 0.2965 time to fit residues: 33.6072 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 : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 50.0000 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 113 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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 = 0.4334 r_free = 0.4334 target = 0.200981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125776 restraints weight = 14673.664| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.63 r_work: 0.3297 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12138 Z= 0.274 Angle : 0.616 8.578 16719 Z= 0.332 Chirality : 0.043 0.277 1799 Planarity : 0.004 0.055 1850 Dihedral : 19.979 178.980 2387 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.58 % Allowed : 23.03 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1171 helix: 1.06 (0.23), residues: 507 sheet: -1.25 (0.46), residues: 130 loop : -1.75 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1252 HIS 0.006 0.001 HIS A1222 PHE 0.016 0.001 PHE A 8 TYR 0.031 0.002 TYR A 628 ARG 0.003 0.001 ARG A 833 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 469) hydrogen bonds : angle 4.88595 ( 1282) covalent geometry : bond 0.00642 (12138) covalent geometry : angle 0.61597 (16719) *********************** 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 111 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 72 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7508 (tmtt) cc_final: 0.6722 (mtmt) REVERT: A 811 LYS cc_start: 0.7608 (tttt) cc_final: 0.7372 (tttp) REVERT: A 1090 ASP cc_start: 0.8324 (t0) cc_final: 0.7467 (p0) REVERT: A 1091 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.6624 (m-10) REVERT: A 1233 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7909 (tp-100) outliers start: 39 outliers final: 23 residues processed: 104 average time/residue: 0.2712 time to fit residues: 40.6021 Evaluate side-chains 89 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 159 THR 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 272 ASN 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 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 1133 GLU 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 123 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.203187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128209 restraints weight = 14795.529| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.63 r_work: 0.3315 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12138 Z= 0.178 Angle : 0.549 8.323 16719 Z= 0.297 Chirality : 0.040 0.192 1799 Planarity : 0.003 0.053 1850 Dihedral : 19.923 178.789 2387 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 3.49 % Allowed : 22.84 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1171 helix: 1.13 (0.23), residues: 506 sheet: -1.11 (0.47), residues: 128 loop : -1.71 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 PHE 0.013 0.001 PHE A1135 TYR 0.026 0.001 TYR A 628 ARG 0.002 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 469) hydrogen bonds : angle 4.59362 ( 1282) covalent geometry : bond 0.00409 (12138) covalent geometry : angle 0.54941 (16719) *********************** 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 110 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7458 (tmtt) cc_final: 0.6681 (mtmt) REVERT: A 272 ASN cc_start: 0.4916 (OUTLIER) cc_final: 0.4555 (p0) REVERT: A 660 ILE cc_start: 0.8227 (mm) cc_final: 0.7993 (mt) REVERT: A 813 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8605 (mttp) REVERT: A 882 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7624 (mmt-90) REVERT: A 1090 ASP cc_start: 0.8310 (t0) cc_final: 0.7462 (p0) REVERT: A 1177 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6775 (pp30) REVERT: A 1233 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7882 (tp-100) outliers start: 38 outliers final: 20 residues processed: 104 average time/residue: 0.2569 time to fit residues: 37.9916 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 : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 116 ASN 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 813 LYS 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 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 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 61 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.203324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126241 restraints weight = 14708.910| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.23 r_work: 0.3298 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12138 Z= 0.256 Angle : 0.605 11.070 16719 Z= 0.323 Chirality : 0.042 0.217 1799 Planarity : 0.004 0.056 1850 Dihedral : 20.038 179.547 2387 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.22 % Allowed : 22.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1171 helix: 1.00 (0.23), residues: 508 sheet: -1.13 (0.47), residues: 128 loop : -1.78 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1252 HIS 0.005 0.001 HIS A1222 PHE 0.015 0.001 PHE A 8 TYR 0.031 0.002 TYR A 628 ARG 0.003 0.000 ARG A 716 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 469) hydrogen bonds : angle 4.64218 ( 1282) covalent geometry : bond 0.00602 (12138) covalent geometry : angle 0.60496 (16719) *********************** 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 111 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7574 (tmtt) cc_final: 0.6779 (mtmt) REVERT: A 302 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.6813 (m-30) REVERT: A 596 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 813 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8348 (mtmp) REVERT: A 882 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7720 (mmt-90) REVERT: A 1090 ASP cc_start: 0.8404 (t0) cc_final: 0.7446 (p0) REVERT: A 1091 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6627 (m-10) REVERT: A 1177 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.6678 (pp30) REVERT: A 1233 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8021 (tp-100) outliers start: 46 outliers final: 26 residues processed: 106 average time/residue: 0.2450 time to fit residues: 37.8013 Evaluate side-chains 97 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 116 ASN 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 302 ASP Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 596 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 813 LYS 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 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 Chi-restraints excluded: chain A residue 1177 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 50.0000 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 37 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4362 r_free = 0.4362 target = 0.203709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126534 restraints weight = 14675.650| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.12 r_work: 0.3356 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12138 Z= 0.147 Angle : 0.534 10.818 16719 Z= 0.288 Chirality : 0.039 0.179 1799 Planarity : 0.003 0.052 1850 Dihedral : 19.910 178.600 2387 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.58 % Allowed : 22.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1171 helix: 1.26 (0.23), residues: 503 sheet: -1.10 (0.47), residues: 128 loop : -1.61 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 PHE 0.013 0.001 PHE A1135 TYR 0.023 0.001 TYR A 628 ARG 0.003 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 469) hydrogen bonds : angle 4.38504 ( 1282) covalent geometry : bond 0.00333 (12138) covalent geometry : angle 0.53421 (16719) *********************** 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 114 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7603 (tmtt) cc_final: 0.6821 (mtmt) REVERT: A 668 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7402 (mtmt) REVERT: A 813 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8351 (mtmp) REVERT: A 826 TYR cc_start: 0.9033 (p90) cc_final: 0.8788 (p90) REVERT: A 1090 ASP cc_start: 0.8263 (t0) cc_final: 0.7408 (p0) REVERT: A 1091 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: A 1233 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7948 (tp-100) outliers start: 39 outliers final: 25 residues processed: 107 average time/residue: 0.2496 time to fit residues: 38.5369 Evaluate side-chains 98 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 116 ASN 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 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 798 ILE Chi-restraints excluded: chain A residue 813 LYS 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 1115 TYR Chi-restraints excluded: chain A residue 1131 VAL 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 59 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.198009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.126538 restraints weight = 14671.132| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.89 r_work: 0.3215 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.006 0.073 12138 Z= 0.270 Angle : 0.621 9.364 16719 Z= 0.331 Chirality : 0.043 0.227 1799 Planarity : 0.004 0.056 1850 Dihedral : 20.106 179.759 2387 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 4.13 % Allowed : 21.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1171 helix: 1.08 (0.23), residues: 502 sheet: -1.16 (0.47), residues: 128 loop : -1.68 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1124 HIS 0.006 0.001 HIS A1222 PHE 0.029 0.002 PHE A1135 TYR 0.031 0.002 TYR A 628 ARG 0.006 0.001 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 469) hydrogen bonds : angle 4.62190 ( 1282) covalent geometry : bond 0.00635 (12138) covalent geometry : angle 0.62139 (16719) *********************** 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 109 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 64 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7233 (tmtt) cc_final: 0.6464 (mtmt) REVERT: A 197 MET cc_start: 0.3308 (tpp) cc_final: 0.2872 (tpt) REVERT: A 302 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: A 361 TYR cc_start: 0.1204 (OUTLIER) cc_final: 0.0832 (m-10) REVERT: A 596 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 813 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8141 (mtmp) REVERT: A 1090 ASP cc_start: 0.8339 (t0) cc_final: 0.7351 (p0) REVERT: A 1091 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6403 (m-10) REVERT: A 1233 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7834 (tp-100) outliers start: 45 outliers final: 32 residues processed: 102 average time/residue: 0.2576 time to fit residues: 37.3974 Evaluate side-chains 100 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 302 ASP Chi-restraints excluded: chain A residue 361 TYR 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 596 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 813 LYS 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 1003 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 59 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1007 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.204118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126261 restraints weight = 14909.863| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.21 r_work: 0.3332 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12138 Z= 0.127 Angle : 0.523 9.087 16719 Z= 0.282 Chirality : 0.038 0.174 1799 Planarity : 0.003 0.051 1850 Dihedral : 19.918 178.467 2387 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.67 % Allowed : 22.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1171 helix: 1.26 (0.23), residues: 507 sheet: -1.12 (0.46), residues: 133 loop : -1.63 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1124 HIS 0.004 0.000 HIS A1222 PHE 0.028 0.001 PHE A1135 TYR 0.019 0.001 TYR A 628 ARG 0.005 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 469) hydrogen bonds : angle 4.32050 ( 1282) covalent geometry : bond 0.00279 (12138) covalent geometry : angle 0.52341 (16719) *********************** 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 112 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7533 (tmtt) cc_final: 0.6742 (mtmt) REVERT: A 813 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8328 (mtmp) REVERT: A 1090 ASP cc_start: 0.8235 (t0) cc_final: 0.7395 (p0) REVERT: A 1091 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: A 1233 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7936 (tp-100) outliers start: 40 outliers final: 27 residues processed: 105 average time/residue: 0.2353 time to fit residues: 36.5936 Evaluate side-chains 95 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 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 798 ILE Chi-restraints excluded: chain A residue 813 LYS 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 1001 ASP Chi-restraints excluded: chain A residue 1003 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 0.0010 chunk 112 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1007 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.204288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131511 restraints weight = 14909.226| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.89 r_work: 0.3319 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12138 Z= 0.174 Angle : 0.571 13.930 16719 Z= 0.301 Chirality : 0.040 0.188 1799 Planarity : 0.003 0.052 1850 Dihedral : 19.906 178.559 2387 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.30 % Allowed : 22.66 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1171 helix: 1.31 (0.23), residues: 503 sheet: -1.15 (0.47), residues: 131 loop : -1.60 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.005 0.001 HIS A1222 PHE 0.024 0.001 PHE A1135 TYR 0.025 0.001 TYR A 628 ARG 0.006 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 469) hydrogen bonds : angle 4.38253 ( 1282) covalent geometry : bond 0.00404 (12138) covalent geometry : angle 0.57112 (16719) *********************** 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: 36 poor density : 68 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7462 (tmtt) cc_final: 0.6690 (mtmt) REVERT: A 596 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 813 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8241 (mtmp) REVERT: A 1090 ASP cc_start: 0.8205 (t0) cc_final: 0.7424 (p0) REVERT: A 1091 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: A 1233 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7869 (tp-100) outliers start: 36 outliers final: 28 residues processed: 97 average time/residue: 0.2482 time to fit residues: 35.4954 Evaluate side-chains 98 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 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 596 LEU Chi-restraints excluded: chain A residue 683 ASP Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 813 LYS 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 1001 ASP Chi-restraints excluded: chain A residue 1003 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 55 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.197514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.126544 restraints weight = 14682.877| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.58 r_work: 0.3208 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 12138 Z= 0.296 Angle : 0.656 13.628 16719 Z= 0.345 Chirality : 0.045 0.229 1799 Planarity : 0.004 0.056 1850 Dihedral : 20.095 179.971 2387 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.49 % Allowed : 22.75 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1171 helix: 1.10 (0.23), residues: 498 sheet: -1.18 (0.47), residues: 128 loop : -1.68 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1124 HIS 0.006 0.001 HIS A1222 PHE 0.023 0.002 PHE A1135 TYR 0.033 0.002 TYR A 628 ARG 0.006 0.001 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 469) hydrogen bonds : angle 4.66754 ( 1282) covalent geometry : bond 0.00700 (12138) covalent geometry : angle 0.65616 (16719) *********************** 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 105 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7357 (tmtt) cc_final: 0.6573 (mtmt) REVERT: A 361 TYR cc_start: 0.1112 (OUTLIER) cc_final: 0.0776 (m-10) REVERT: A 596 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 813 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8231 (mtmp) REVERT: A 1090 ASP cc_start: 0.8412 (t0) cc_final: 0.7376 (p0) REVERT: A 1091 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: A 1233 GLN cc_start: 0.8411 (tp-100) cc_final: 0.7976 (tp-100) outliers start: 38 outliers final: 33 residues processed: 99 average time/residue: 0.2437 time to fit residues: 35.4819 Evaluate side-chains 101 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 243 THR Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 361 TYR 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 596 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 813 LYS 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 1001 ASP Chi-restraints excluded: chain A residue 1003 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 1131 VAL Chi-restraints excluded: chain A residue 1133 GLU 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 102 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 0.0870 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A1007 ASN A1244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.204733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127598 restraints weight = 14770.114| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.50 r_work: 0.3306 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12138 Z= 0.146 Angle : 0.560 13.431 16719 Z= 0.297 Chirality : 0.040 0.188 1799 Planarity : 0.003 0.052 1850 Dihedral : 19.941 179.139 2387 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.21 % Allowed : 23.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1171 helix: 1.26 (0.23), residues: 501 sheet: -1.05 (0.47), residues: 128 loop : -1.61 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 PHE 0.023 0.001 PHE A1135 TYR 0.022 0.001 TYR A 628 ARG 0.009 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 469) hydrogen bonds : angle 4.40059 ( 1282) covalent geometry : bond 0.00331 (12138) covalent geometry : angle 0.55993 (16719) ********************** 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 99 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 64 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7443 (tmtt) cc_final: 0.6701 (mtmt) REVERT: A 668 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7442 (mtmt) REVERT: A 813 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8242 (mtmp) REVERT: A 1023 GLU cc_start: 0.7678 (mp0) cc_final: 0.7319 (mp0) REVERT: A 1090 ASP cc_start: 0.8218 (t0) cc_final: 0.7419 (p0) REVERT: A 1091 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: A 1233 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7845 (tp-100) outliers start: 35 outliers final: 29 residues processed: 93 average time/residue: 0.2518 time to fit residues: 33.9072 Evaluate side-chains 97 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN 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 272 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN 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 813 LYS 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 1001 ASP Chi-restraints excluded: chain A residue 1003 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 1131 VAL Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 55 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 113 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.202877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127142 restraints weight = 14706.242| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.70 r_work: 0.3276 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1843 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= 0.160 Angle : 0.564 13.213 16719 Z= 0.298 Chirality : 0.040 0.186 1799 Planarity : 0.004 0.068 1850 Dihedral : 19.909 178.749 2387 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.12 % Allowed : 23.39 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1171 helix: 1.30 (0.23), residues: 501 sheet: -1.09 (0.47), residues: 129 loop : -1.60 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1124 HIS 0.005 0.001 HIS A1222 PHE 0.022 0.001 PHE A1135 TYR 0.023 0.001 TYR A 628 ARG 0.015 0.000 ARG A1173 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 469) hydrogen bonds : angle 4.38011 ( 1282) covalent geometry : bond 0.00366 (12138) covalent geometry : angle 0.56386 (16719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6724.93 seconds wall clock time: 117 minutes 3.66 seconds (7023.66 seconds total)