Starting phenix.real_space_refine on Sat Oct 12 06:41:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qwe_18693/10_2024/8qwe_18693.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qwe_18693/10_2024/8qwe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qwe_18693/10_2024/8qwe_18693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qwe_18693/10_2024/8qwe_18693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qwe_18693/10_2024/8qwe_18693.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qwe_18693/10_2024/8qwe_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 8.57, per 1000 atoms: 0.73 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: 3.96 Conformation dependent library (CDL) restraints added in 1.5 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: 5.46 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: 6.77 Time building geometry restraints manager: 4.45 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: 0.010 Normalize map: mean=0, sd=1: 4.280 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 40.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- 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= 0.417 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.263 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: 0.3376 time to fit residues: 38.1291 Evaluate side-chains 68 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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= 0.397 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 *********************** 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 fitting. rotamer outliers: 39 poor density : 72 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7597 (tmtt) cc_final: 0.6786 (mtmt) REVERT: A 811 LYS cc_start: 0.7688 (tttt) cc_final: 0.7447 (tttp) REVERT: A 1090 ASP cc_start: 0.8319 (t0) cc_final: 0.7447 (p0) REVERT: A 1091 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6567 (m-10) REVERT: A 1173 ARG cc_start: 0.7058 (mtm-85) cc_final: 0.6852 (mtm-85) REVERT: A 1233 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7766 (tp-100) outliers start: 39 outliers final: 23 residues processed: 104 average time/residue: 0.2847 time to fit residues: 42.3329 Evaluate side-chains 89 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.0020 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12138 Z= 0.155 Angle : 0.514 8.273 16719 Z= 0.279 Chirality : 0.038 0.165 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.832 177.993 2387 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.75 % Allowed : 23.39 % 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: -0.41 (0.25), residues: 1171 helix: 1.28 (0.23), residues: 505 sheet: -1.08 (0.48), residues: 126 loop : -1.62 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.002 0.000 HIS A1222 PHE 0.013 0.001 PHE A1135 TYR 0.019 0.001 TYR A 628 ARG 0.003 0.000 ARG A 716 *********************** 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 108 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 0.966 Fit side-chains REVERT: A 108 LYS cc_start: 0.7523 (tmtt) cc_final: 0.6725 (mtmt) REVERT: A 272 ASN cc_start: 0.4741 (OUTLIER) cc_final: 0.4466 (p0) REVERT: A 660 ILE cc_start: 0.8192 (mm) cc_final: 0.7919 (mm) REVERT: A 882 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7295 (mmt-90) REVERT: A 1090 ASP cc_start: 0.8229 (t0) cc_final: 0.7431 (p0) REVERT: A 1173 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6625 (mtm-85) REVERT: A 1233 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7699 (tp-100) outliers start: 30 outliers final: 12 residues processed: 102 average time/residue: 0.2809 time to fit residues: 40.9292 Evaluate side-chains 84 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 622 CYS 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 1094 PHE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1157 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 50.0000 chunk 100 optimal weight: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12138 Z= 0.375 Angle : 0.605 11.051 16719 Z= 0.322 Chirality : 0.042 0.220 1799 Planarity : 0.004 0.054 1850 Dihedral : 19.997 179.217 2387 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.67 % Allowed : 22.57 % 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: -0.62 (0.25), residues: 1171 helix: 1.07 (0.23), residues: 508 sheet: -1.11 (0.47), residues: 128 loop : -1.74 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1252 HIS 0.006 0.001 HIS A1222 PHE 0.016 0.001 PHE A 8 TYR 0.032 0.002 TYR A 628 ARG 0.003 0.000 ARG A 833 *********************** 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 109 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 69 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7552 (tmtt) cc_final: 0.6759 (mtmt) REVERT: A 272 ASN cc_start: 0.4698 (OUTLIER) cc_final: 0.4381 (p0) REVERT: A 882 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7419 (mmt-90) REVERT: A 1090 ASP cc_start: 0.8272 (t0) cc_final: 0.7424 (p0) REVERT: A 1091 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6615 (m-10) REVERT: A 1173 ARG cc_start: 0.6629 (mtm-85) cc_final: 0.6419 (mtm-85) REVERT: A 1233 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7754 (tp-100) outliers start: 40 outliers final: 24 residues processed: 104 average time/residue: 0.2677 time to fit residues: 40.1048 Evaluate side-chains 95 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 255 ILE Chi-restraints excluded: chain A residue 272 ASN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1348 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= 0.210 Angle : 0.538 11.125 16719 Z= 0.289 Chirality : 0.039 0.185 1799 Planarity : 0.003 0.051 1850 Dihedral : 19.911 178.725 2387 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.12 % Allowed : 22.75 % 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: -0.38 (0.25), residues: 1171 helix: 1.28 (0.23), residues: 500 sheet: -1.05 (0.47), residues: 128 loop : -1.56 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 PHE 0.012 0.001 PHE A1135 TYR 0.023 0.001 TYR A 628 ARG 0.001 0.000 ARG A 833 *********************** 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 108 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 74 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7546 (tmtt) cc_final: 0.6750 (mtmt) REVERT: A 272 ASN cc_start: 0.4567 (OUTLIER) cc_final: 0.4239 (p0) REVERT: A 668 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7530 (mtmt) REVERT: A 1090 ASP cc_start: 0.8168 (t0) cc_final: 0.7385 (p0) REVERT: A 1091 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6522 (m-10) REVERT: A 1233 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7697 (tp-100) outliers start: 34 outliers final: 24 residues processed: 101 average time/residue: 0.1979 time to fit residues: 28.9820 Evaluate side-chains 97 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 70 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 116 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1394 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= 0.171 Angle : 0.517 10.011 16719 Z= 0.279 Chirality : 0.038 0.173 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.847 178.090 2387 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.84 % Allowed : 22.66 % 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: -0.36 (0.25), residues: 1171 helix: 1.32 (0.23), residues: 507 sheet: -1.06 (0.47), residues: 131 loop : -1.60 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1124 HIS 0.003 0.000 HIS A1222 PHE 0.012 0.001 PHE A1135 TYR 0.020 0.001 TYR A 628 ARG 0.007 0.000 ARG A1173 *********************** 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 fitting. rotamer outliers: 31 poor density : 78 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7521 (tmtt) cc_final: 0.6727 (mtmt) REVERT: A 272 ASN cc_start: 0.4529 (OUTLIER) cc_final: 0.4227 (p0) REVERT: A 668 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7558 (mtmt) REVERT: A 1090 ASP cc_start: 0.8144 (t0) cc_final: 0.7363 (p0) REVERT: A 1091 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6616 (m-10) REVERT: A 1173 ARG cc_start: 0.6380 (mtm-85) cc_final: 0.6180 (mtm-85) REVERT: A 1233 GLN cc_start: 0.7959 (tp-100) cc_final: 0.7642 (tp-100) outliers start: 31 outliers final: 23 residues processed: 102 average time/residue: 0.2444 time to fit residues: 36.7001 Evaluate side-chains 99 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 73 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 272 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 456 GLN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12138 Z= 0.184 Angle : 0.526 9.487 16719 Z= 0.281 Chirality : 0.038 0.173 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.827 177.976 2387 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % 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 (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: -0.34 (0.25), residues: 1171 helix: 1.36 (0.23), residues: 507 sheet: -1.09 (0.47), residues: 129 loop : -1.60 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1124 HIS 0.004 0.000 HIS A1222 PHE 0.033 0.001 PHE A1135 TYR 0.021 0.001 TYR A 628 ARG 0.004 0.000 ARG A1173 *********************** 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 113 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7543 (tmtt) cc_final: 0.6726 (mtmt) REVERT: A 272 ASN cc_start: 0.4462 (OUTLIER) cc_final: 0.4203 (p0) REVERT: A 596 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 668 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7577 (mtmt) REVERT: A 1090 ASP cc_start: 0.8134 (t0) cc_final: 0.7378 (p0) REVERT: A 1091 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: A 1233 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7627 (tp-100) outliers start: 40 outliers final: 27 residues processed: 106 average time/residue: 0.2400 time to fit residues: 37.0935 Evaluate side-chains 100 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 69 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN ** A 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12138 Z= 0.218 Angle : 0.536 9.179 16719 Z= 0.286 Chirality : 0.039 0.179 1799 Planarity : 0.003 0.048 1850 Dihedral : 19.800 178.156 2387 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.03 % Allowed : 22.66 % 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 (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: -0.35 (0.25), residues: 1171 helix: 1.33 (0.23), residues: 507 sheet: -1.10 (0.46), residues: 131 loop : -1.59 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.004 0.001 HIS A1222 PHE 0.027 0.001 PHE A1135 TYR 0.023 0.001 TYR A 628 ARG 0.005 0.000 ARG A1173 *********************** 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 109 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7560 (tmtt) cc_final: 0.6767 (mtmt) REVERT: A 272 ASN cc_start: 0.4566 (OUTLIER) cc_final: 0.4266 (p0) REVERT: A 596 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8649 (mt) REVERT: A 668 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7554 (mtmt) REVERT: A 1090 ASP cc_start: 0.8142 (t0) cc_final: 0.7384 (p0) REVERT: A 1091 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6579 (m-10) REVERT: A 1178 MET cc_start: 0.8321 (mpp) cc_final: 0.7964 (mtm) REVERT: A 1233 GLN cc_start: 0.7930 (tp-100) cc_final: 0.7613 (tp-100) outliers start: 33 outliers final: 27 residues processed: 101 average time/residue: 0.2420 time to fit residues: 36.3087 Evaluate side-chains 103 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 72 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 GLU 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 986 GLN A1007 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12138 Z= 0.185 Angle : 0.528 8.994 16719 Z= 0.282 Chirality : 0.039 0.190 1799 Planarity : 0.003 0.048 1850 Dihedral : 19.761 178.025 2387 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.03 % Allowed : 22.57 % 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 (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: -0.30 (0.25), residues: 1171 helix: 1.40 (0.23), residues: 506 sheet: -1.15 (0.46), residues: 131 loop : -1.56 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1124 HIS 0.004 0.000 HIS A1222 PHE 0.024 0.001 PHE A1135 TYR 0.021 0.001 TYR A 628 ARG 0.006 0.000 ARG A1173 *********************** 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 fitting. rotamer outliers: 33 poor density : 72 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LYS cc_start: 0.7550 (tmtt) cc_final: 0.6739 (mtmt) REVERT: A 272 ASN cc_start: 0.4551 (OUTLIER) cc_final: 0.4264 (p0) REVERT: A 596 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 668 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7560 (mtmt) REVERT: A 957 MET cc_start: 0.8723 (ttp) cc_final: 0.8513 (ptm) REVERT: A 1090 ASP cc_start: 0.8118 (t0) cc_final: 0.7407 (p0) REVERT: A 1091 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6601 (m-10) REVERT: A 1178 MET cc_start: 0.8259 (mpp) cc_final: 0.7932 (mtm) REVERT: A 1233 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7635 (tp-100) outliers start: 33 outliers final: 25 residues processed: 97 average time/residue: 0.2558 time to fit residues: 36.5333 Evaluate side-chains 96 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 67 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 0.005 0.054 12138 Z= 0.301 Angle : 0.578 8.837 16719 Z= 0.308 Chirality : 0.041 0.199 1799 Planarity : 0.003 0.049 1850 Dihedral : 19.853 178.775 2387 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.94 % Allowed : 22.84 % 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 (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: -0.36 (0.25), residues: 1171 helix: 1.35 (0.23), residues: 501 sheet: -1.19 (0.47), residues: 131 loop : -1.56 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1124 HIS 0.005 0.001 HIS A1222 PHE 0.023 0.001 PHE A1135 TYR 0.027 0.001 TYR A 628 ARG 0.008 0.000 ARG A1173 ********************** 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 104 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8177 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: A 108 LYS cc_start: 0.7565 (tmtt) cc_final: 0.6774 (mtmt) REVERT: A 272 ASN cc_start: 0.4670 (OUTLIER) cc_final: 0.4337 (p0) REVERT: A 596 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8674 (mt) REVERT: A 668 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7550 (mtmt) REVERT: A 1090 ASP cc_start: 0.8212 (t0) cc_final: 0.7486 (p0) REVERT: A 1091 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: A 1233 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7670 (tp-100) outliers start: 32 outliers final: 25 residues processed: 96 average time/residue: 0.2534 time to fit residues: 35.9361 Evaluate side-chains 102 residues out of total 1090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 73 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.204924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.127883 restraints weight = 14613.064| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.28 r_work: 0.3335 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1687 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= 0.178 Angle : 0.533 8.830 16719 Z= 0.285 Chirality : 0.039 0.183 1799 Planarity : 0.003 0.048 1850 Dihedral : 19.778 178.231 2387 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.84 % Allowed : 22.75 % 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 (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: -0.31 (0.25), residues: 1171 helix: 1.38 (0.23), residues: 506 sheet: -1.16 (0.47), residues: 131 loop : -1.55 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1124 HIS 0.004 0.000 HIS A1222 PHE 0.027 0.001 PHE A1135 TYR 0.021 0.001 TYR A 628 ARG 0.009 0.000 ARG A1173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.89 seconds wall clock time: 54 minutes 36.54 seconds (3276.54 seconds total)