Starting phenix.real_space_refine on Fri Sep 11 19:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d4b_27180/09_2026/8d4b_27180.map" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 25 5.16 5 C 6729 2.51 5 N 1887 2.21 5 O 2301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11010 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9547 Classifications: {'peptide': 1166} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 1137} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 870 Classifications: {'RNAv2': 41} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 593 Classifications: {'RNAv2': 28} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 8, 'rna3p_pyr': 15} Link IDs: {'rna2p': 4, 'rna3p': 23} Time building chain proxies: 2.04, per 1000 atoms: 0.19 Number of scatterers: 11010 At special positions: 0 Unit cell: (85.86, 107.73, 117.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 68 15.00 O 2301 8.00 N 1887 7.00 C 6729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 485.1 milliseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 55.8% alpha, 13.0% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.714A pdb=" N SER A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 79 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 127 through 162 removed outlier: 3.686A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 170 removed outlier: 3.719A pdb=" N ALA A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 4.050A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.585A pdb=" N ILE A 204 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 206' Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.685A pdb=" N ILE A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 239 removed outlier: 4.268A pdb=" N LEU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.604A pdb=" N LYS A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 376 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 418 through 438 Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.936A pdb=" N LEU A 443 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 487 through 504 Processing helix chain 'A' and resid 529 through 557 removed outlier: 3.889A pdb=" N LEU A 533 " --> pdb=" O PRO A 529 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.622A pdb=" N LEU A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.609A pdb=" N ASN A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 654 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 674 Processing helix chain 'A' and resid 675 through 681 removed outlier: 3.586A pdb=" N LYS A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.576A pdb=" N GLY A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 707 Processing helix chain 'A' and resid 716 through 726 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.678A pdb=" N PHE A 757 " --> pdb=" O TRP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.547A pdb=" N GLU A 814 " --> pdb=" O LYS A 810 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 837 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 940 through 961 removed outlier: 3.632A pdb=" N LYS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 974 through 983 Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.843A pdb=" N GLU A1005 " --> pdb=" O ASN A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1018 No H-bonds generated for 'chain 'A' and resid 1016 through 1018' Processing helix chain 'A' and resid 1019 through 1028 removed outlier: 3.772A pdb=" N ILE A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1054 removed outlier: 3.670A pdb=" N MET A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1105 through 1118 removed outlier: 3.556A pdb=" N PHE A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1209 Processing helix chain 'A' and resid 1213 through 1232 removed outlier: 3.536A pdb=" N SER A1224 " --> pdb=" O ILE A1220 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A1227 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A1232 " --> pdb=" O LEU A1228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18 removed outlier: 6.884A pdb=" N GLN A 790 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 772 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 792 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 770 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA A 794 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 768 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 796 " --> pdb=" O HIS A 766 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 250 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE A 769 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS A 248 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 771 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 566 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 18 removed outlier: 6.884A pdb=" N GLN A 790 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 772 " --> pdb=" O GLN A 790 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 792 " --> pdb=" O ALA A 770 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA A 770 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA A 794 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLU A 768 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN A 796 " --> pdb=" O HIS A 766 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 250 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE A 769 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS A 248 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL A 771 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 566 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 899 through 900 removed outlier: 4.597A pdb=" N GLU A1063 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 887 through 896 removed outlier: 5.603A pdb=" N TRP A 888 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 878 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N HIS A 890 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLU A 876 " --> pdb=" O HIS A 890 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLN A 892 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS A 874 " --> pdb=" O GLN A 892 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU A 871 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 916 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS A 875 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AA7, first strand: chain 'A' and resid 1120 through 1121 498 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2655 1.33 - 1.45: 2591 1.45 - 1.57: 5953 1.57 - 1.69: 135 1.69 - 1.81: 37 Bond restraints: 11371 Sorted by residual: bond pdb=" CG1 ILE A1220 " pdb=" CD1 ILE A1220 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.96e+00 bond pdb=" CG LEU A 966 " pdb=" CD1 LEU A 966 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.96e+00 bond pdb=" C VAL A1130 " pdb=" N PRO A1131 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.26e-02 6.30e+03 1.92e+00 bond pdb=" C HIS A 374 " pdb=" N TYR A 375 " ideal model delta sigma weight residual 1.333 1.295 0.038 2.74e-02 1.33e+03 1.90e+00 bond pdb=" CB MET A 958 " pdb=" CG MET A 958 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.83e+00 ... (remaining 11366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15078 1.88 - 3.76: 478 3.76 - 5.65: 79 5.65 - 7.53: 13 7.53 - 9.41: 1 Bond angle restraints: 15649 Sorted by residual: angle pdb=" CA GLU A1063 " pdb=" CB GLU A1063 " pdb=" CG GLU A1063 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" OG1 THR A 239 " pdb=" CB THR A 239 " pdb=" CG2 THR A 239 " ideal model delta sigma weight residual 109.30 103.31 5.99 2.00e+00 2.50e-01 8.96e+00 angle pdb=" OG1 THR A 50 " pdb=" CB THR A 50 " pdb=" CG2 THR A 50 " ideal model delta sigma weight residual 109.30 103.32 5.98 2.00e+00 2.50e-01 8.93e+00 angle pdb=" C VAL A 415 " pdb=" N SER A 416 " pdb=" CA SER A 416 " ideal model delta sigma weight residual 125.66 131.13 -5.47 1.85e+00 2.92e-01 8.74e+00 angle pdb=" OG1 THR A 628 " pdb=" CB THR A 628 " pdb=" CG2 THR A 628 " ideal model delta sigma weight residual 109.30 103.51 5.79 2.00e+00 2.50e-01 8.38e+00 ... (remaining 15644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 5915 16.30 - 32.60: 561 32.60 - 48.90: 177 48.90 - 65.20: 59 65.20 - 81.50: 27 Dihedral angle restraints: 6739 sinusoidal: 3294 harmonic: 3445 Sorted by residual: dihedral pdb=" C4' A C 23 " pdb=" C3' A C 23 " pdb=" C2' A C 23 " pdb=" C1' A C 23 " ideal model delta sinusoidal sigma weight residual 36.34 -39.22 75.56 1 3.10e+00 1.04e-01 7.50e+02 dihedral pdb=" C4' U B 5 " pdb=" C3' U B 5 " pdb=" C2' U B 5 " pdb=" C1' U B 5 " ideal model delta sinusoidal sigma weight residual 36.34 -37.20 73.54 1 3.10e+00 1.04e-01 7.16e+02 dihedral pdb=" C4' U B 22 " pdb=" C3' U B 22 " pdb=" C2' U B 22 " pdb=" C1' U B 22 " ideal model delta sinusoidal sigma weight residual 36.34 -37.19 73.53 1 3.10e+00 1.04e-01 7.16e+02 ... (remaining 6736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1432 0.061 - 0.122: 216 0.122 - 0.183: 23 0.183 - 0.244: 68 0.244 - 0.305: 19 Chirality restraints: 1758 Sorted by residual: chirality pdb=" C2' A B 13 " pdb=" C3' A B 13 " pdb=" O2' A B 13 " pdb=" C1' A B 13 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C2' U B 5 " pdb=" C3' U B 5 " pdb=" O2' U B 5 " pdb=" C1' U B 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C3' G C 21 " pdb=" C4' G C 21 " pdb=" O3' G C 21 " pdb=" C2' G C 21 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1755 not shown) Planarity restraints: 1759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 426 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" CG ASP A 426 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP A 426 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 426 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1063 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" CD GLU A1063 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU A1063 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU A1063 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 192 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 193 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.025 5.00e-02 4.00e+02 ... (remaining 1756 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 85 2.53 - 3.13: 7930 3.13 - 3.72: 18262 3.72 - 4.31: 27263 4.31 - 4.90: 42980 Nonbonded interactions: 96520 Sorted by model distance: nonbonded pdb=" OD1 ASP A 209 " pdb=" CD1 ILE A 216 " model vdw 1.942 3.460 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASP A 426 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR A 627 " pdb=" O2' A C 24 " model vdw 2.211 3.040 nonbonded pdb=" O ASP A 235 " pdb=" CG2 THR A 239 " model vdw 2.230 3.460 nonbonded pdb=" O ILE A 986 " pdb=" OH TYR A 995 " model vdw 2.245 3.040 ... (remaining 96515 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.010 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 0.055 11371 Z= 0.220 Angle : 0.788 9.410 15649 Z= 0.413 Chirality : 0.068 0.305 1758 Planarity : 0.004 0.044 1759 Dihedral : 15.414 81.501 4513 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1158 helix: -0.73 (0.19), residues: 597 sheet: -1.26 (0.41), residues: 141 loop : -1.28 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 928 TYR 0.024 0.002 TYR A 157 PHE 0.027 0.002 PHE A 806 TRP 0.017 0.002 TRP A 888 HIS 0.006 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.22 (11371) covalent geometry : angle 0.78751 / 0.41 (15649) hydrogen bonds : bond 0.17780 / 11.64 ( 543) hydrogen bonds : angle 7.05995 / 4.84 ( 1531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 485 HIS cc_start: 0.6845 (m90) cc_final: 0.6163 (m90) outliers start: 0 outliers final: 1 residues processed: 105 average time/residue: 0.7044 time to fit residues: 78.7116 Evaluate side-chains 34 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 109 GLN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.081208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067417 restraints weight = 26459.721| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.66 r_work: 0.2918 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11371 Z= 0.187 Angle : 0.771 14.946 15649 Z= 0.357 Chirality : 0.068 1.098 1758 Planarity : 0.004 0.036 1759 Dihedral : 12.285 145.635 2085 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.95 % Allowed : 6.47 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.24), residues: 1158 helix: 0.27 (0.20), residues: 605 sheet: -1.17 (0.44), residues: 131 loop : -1.01 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 307 TYR 0.018 0.001 TYR A 544 PHE 0.015 0.001 PHE A 180 TRP 0.012 0.001 TRP A 888 HIS 0.004 0.001 HIS A 755 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (11371) covalent geometry : angle 0.77096 / 0.36 (15649) hydrogen bonds : bond 0.05104 / 3.57 ( 543) hydrogen bonds : angle 4.66424 / 3.21 ( 1531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.429 Fit side-chains REVERT: A 122 MET cc_start: 0.8599 (mmm) cc_final: 0.8240 (tpp) REVERT: A 215 LEU cc_start: 0.8184 (tt) cc_final: 0.7897 (tm) REVERT: A 831 LYS cc_start: 0.9122 (tptt) cc_final: 0.8826 (ttpp) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.5688 time to fit residues: 39.7427 Evaluate side-chains 41 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1077 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN A 447 GLN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.064448 restraints weight = 26959.643| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.72 r_work: 0.2846 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 11371 Z= 0.264 Angle : 0.739 13.630 15649 Z= 0.346 Chirality : 0.065 0.935 1758 Planarity : 0.003 0.044 1759 Dihedral : 11.776 142.290 2083 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.24 % Allowed : 8.37 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.25), residues: 1158 helix: 0.65 (0.21), residues: 609 sheet: -1.25 (0.46), residues: 132 loop : -0.87 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.020 0.002 TYR A 544 PHE 0.017 0.002 PHE A 757 TRP 0.010 0.001 TRP A 888 HIS 0.014 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (11371) covalent geometry : angle 0.73927 / 0.35 (15649) hydrogen bonds : bond 0.04950 / 3.42 ( 543) hydrogen bonds : angle 4.42761 / 3.07 ( 1531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.455 Fit side-chains REVERT: A 122 MET cc_start: 0.8692 (mmm) cc_final: 0.8296 (tpp) REVERT: A 215 LEU cc_start: 0.8256 (tt) cc_final: 0.8024 (tm) REVERT: A 488 LYS cc_start: 0.8577 (tppt) cc_final: 0.8339 (tppp) REVERT: A 831 LYS cc_start: 0.9135 (tptt) cc_final: 0.8867 (ttpp) REVERT: A 1211 ASN cc_start: 0.8106 (t0) cc_final: 0.7858 (t0) outliers start: 13 outliers final: 5 residues processed: 48 average time/residue: 0.6487 time to fit residues: 33.9206 Evaluate side-chains 37 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 872 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.081339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067636 restraints weight = 26601.074| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.70 r_work: 0.2913 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11371 Z= 0.145 Angle : 0.626 10.286 15649 Z= 0.293 Chirality : 0.055 0.594 1758 Planarity : 0.003 0.040 1759 Dihedral : 11.722 137.648 2083 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.33 % Allowed : 9.13 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.25), residues: 1158 helix: 1.06 (0.21), residues: 608 sheet: -1.09 (0.46), residues: 131 loop : -0.71 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.017 0.001 TYR A 544 PHE 0.013 0.001 PHE A 180 TRP 0.009 0.001 TRP A 888 HIS 0.004 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11371) covalent geometry : angle 0.62617 / 0.29 (15649) hydrogen bonds : bond 0.04469 / 3.23 ( 543) hydrogen bonds : angle 4.14119 / 2.88 ( 1531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 1211 ASN cc_start: 0.8018 (t0) cc_final: 0.7719 (t0) outliers start: 14 outliers final: 6 residues processed: 54 average time/residue: 0.4997 time to fit residues: 29.6892 Evaluate side-chains 42 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 1 optimal weight: 0.0570 chunk 118 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.066733 restraints weight = 26556.377| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.71 r_work: 0.2896 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11371 Z= 0.167 Angle : 0.641 9.485 15649 Z= 0.298 Chirality : 0.055 0.594 1758 Planarity : 0.003 0.042 1759 Dihedral : 11.700 139.368 2083 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.95 % Allowed : 10.56 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.25), residues: 1158 helix: 1.23 (0.21), residues: 608 sheet: -1.02 (0.47), residues: 130 loop : -0.66 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.018 0.001 TYR A 544 PHE 0.014 0.001 PHE A 180 TRP 0.008 0.001 TRP A 385 HIS 0.008 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (11371) covalent geometry : angle 0.64054 / 0.30 (15649) hydrogen bonds : bond 0.04415 / 3.15 ( 543) hydrogen bonds : angle 4.09371 / 2.84 ( 1531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.315 Fit side-chains REVERT: A 831 LYS cc_start: 0.9151 (tptt) cc_final: 0.8833 (ttpp) REVERT: A 1211 ASN cc_start: 0.7999 (t0) cc_final: 0.7679 (t0) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.4408 time to fit residues: 21.0753 Evaluate side-chains 42 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 872 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 0.0770 chunk 46 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069303 restraints weight = 26455.400| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.71 r_work: 0.2955 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11371 Z= 0.110 Angle : 0.592 8.876 15649 Z= 0.276 Chirality : 0.051 0.498 1758 Planarity : 0.003 0.037 1759 Dihedral : 11.697 139.855 2083 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.05 % Allowed : 10.47 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1158 helix: 1.43 (0.21), residues: 609 sheet: -0.95 (0.47), residues: 130 loop : -0.57 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.015 0.001 TYR A 544 PHE 0.012 0.001 PHE A 180 TRP 0.009 0.001 TRP A 888 HIS 0.009 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (11371) covalent geometry : angle 0.59244 / 0.28 (15649) hydrogen bonds : bond 0.04229 / 3.11 ( 543) hydrogen bonds : angle 3.94133 / 2.73 ( 1531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.402 Fit side-chains REVERT: A 831 LYS cc_start: 0.9112 (tptt) cc_final: 0.8805 (ttpp) REVERT: A 871 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: A 1211 ASN cc_start: 0.7968 (t0) cc_final: 0.7642 (t0) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 0.4956 time to fit residues: 28.5727 Evaluate side-chains 40 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 89 optimal weight: 0.0050 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.066998 restraints weight = 26580.353| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.75 r_work: 0.2904 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11371 Z= 0.174 Angle : 0.628 8.705 15649 Z= 0.293 Chirality : 0.054 0.573 1758 Planarity : 0.003 0.041 1759 Dihedral : 11.677 142.007 2083 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.33 % Allowed : 11.04 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1158 helix: 1.41 (0.21), residues: 612 sheet: -1.00 (0.47), residues: 130 loop : -0.55 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.019 0.001 TYR A 544 PHE 0.015 0.001 PHE A 180 TRP 0.010 0.001 TRP A 655 HIS 0.007 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (11371) covalent geometry : angle 0.62812 / 0.29 (15649) hydrogen bonds : bond 0.04337 / 3.10 ( 543) hydrogen bonds : angle 3.99990 / 2.78 ( 1531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.254 Fit side-chains REVERT: A 831 LYS cc_start: 0.9117 (tptt) cc_final: 0.8866 (ttpp) REVERT: A 871 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: A 1211 ASN cc_start: 0.7905 (t0) cc_final: 0.7594 (t0) outliers start: 14 outliers final: 8 residues processed: 43 average time/residue: 0.4637 time to fit residues: 22.3505 Evaluate side-chains 43 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.081851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067978 restraints weight = 26433.894| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.73 r_work: 0.2928 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11371 Z= 0.138 Angle : 0.608 10.670 15649 Z= 0.282 Chirality : 0.052 0.532 1758 Planarity : 0.003 0.038 1759 Dihedral : 11.679 141.782 2083 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.14 % Allowed : 11.32 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1158 helix: 1.50 (0.21), residues: 613 sheet: -0.98 (0.46), residues: 130 loop : -0.48 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 307 TYR 0.017 0.001 TYR A 544 PHE 0.013 0.001 PHE A 180 TRP 0.007 0.001 TRP A 385 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11371) covalent geometry : angle 0.60789 / 0.28 (15649) hydrogen bonds : bond 0.04250 / 3.08 ( 543) hydrogen bonds : angle 3.92421 / 2.72 ( 1531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.356 Fit side-chains REVERT: A 831 LYS cc_start: 0.9068 (tptt) cc_final: 0.8866 (ttpp) REVERT: A 1211 ASN cc_start: 0.7923 (t0) cc_final: 0.7616 (t0) outliers start: 12 outliers final: 7 residues processed: 45 average time/residue: 0.4477 time to fit residues: 22.5922 Evaluate side-chains 42 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 24 optimal weight: 0.0770 chunk 91 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.083929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.070164 restraints weight = 26186.865| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.73 r_work: 0.2970 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11371 Z= 0.108 Angle : 0.586 9.734 15649 Z= 0.272 Chirality : 0.050 0.451 1758 Planarity : 0.003 0.036 1759 Dihedral : 11.636 142.046 2083 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.95 % Allowed : 11.51 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1158 helix: 1.61 (0.21), residues: 613 sheet: -0.95 (0.46), residues: 130 loop : -0.45 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.015 0.001 TYR A 544 PHE 0.011 0.001 PHE A 180 TRP 0.008 0.001 TRP A 888 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (11371) covalent geometry : angle 0.58561 / 0.27 (15649) hydrogen bonds : bond 0.04130 / 3.04 ( 543) hydrogen bonds : angle 3.82919 / 2.66 ( 1531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.403 Fit side-chains REVERT: A 1043 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: A 1211 ASN cc_start: 0.7907 (t0) cc_final: 0.7593 (t0) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.4076 time to fit residues: 19.9907 Evaluate side-chains 40 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 82 optimal weight: 0.0070 chunk 28 optimal weight: 5.9990 chunk 98 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 0.0570 chunk 14 optimal weight: 2.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069306 restraints weight = 26662.453| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.77 r_work: 0.2956 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11371 Z= 0.127 Angle : 0.600 12.570 15649 Z= 0.279 Chirality : 0.050 0.470 1758 Planarity : 0.003 0.035 1759 Dihedral : 11.608 142.335 2083 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.76 % Allowed : 12.18 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.26), residues: 1158 helix: 1.65 (0.21), residues: 613 sheet: -0.96 (0.46), residues: 130 loop : -0.46 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 307 TYR 0.017 0.001 TYR A 544 PHE 0.013 0.001 PHE A 180 TRP 0.007 0.001 TRP A 385 HIS 0.006 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (11371) covalent geometry : angle 0.59972 / 0.28 (15649) hydrogen bonds : bond 0.04128 / 3.01 ( 543) hydrogen bonds : angle 3.83342 / 2.66 ( 1531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.395 Fit side-chains REVERT: A 831 LYS cc_start: 0.9113 (tptt) cc_final: 0.8810 (ttpp) REVERT: A 1211 ASN cc_start: 0.7930 (t0) cc_final: 0.7608 (t0) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.3998 time to fit residues: 19.2192 Evaluate side-chains 42 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 GLN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.063363 restraints weight = 27064.447| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.73 r_work: 0.2828 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11371 Z= 0.334 Angle : 0.760 11.875 15649 Z= 0.355 Chirality : 0.063 0.773 1758 Planarity : 0.003 0.048 1759 Dihedral : 11.774 142.384 2083 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.76 % Allowed : 11.99 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1158 helix: 1.31 (0.21), residues: 609 sheet: -1.26 (0.44), residues: 132 loop : -0.68 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 307 TYR 0.021 0.002 TYR A 544 PHE 0.016 0.002 PHE A 180 TRP 0.010 0.002 TRP A 480 HIS 0.009 0.001 HIS A 587 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.33 (11371) covalent geometry : angle 0.75982 / 0.35 (15649) hydrogen bonds : bond 0.04812 / 3.31 ( 543) hydrogen bonds : angle 4.27993 / 2.97 ( 1531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.29 seconds wall clock time: 39 minutes 51.48 seconds (2391.48 seconds total)