Starting phenix.real_space_refine on Sat Nov 16 14:29:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4b_27180/11_2024/8d4b_27180.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4b_27180/11_2024/8d4b_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4b_27180/11_2024/8d4b_27180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4b_27180/11_2024/8d4b_27180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4b_27180/11_2024/8d4b_27180.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4b_27180/11_2024/8d4b_27180.cif" } resolution = 2.92 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'RNA': 41} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 593 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 8, 'rna3p_pyr': 15} Link IDs: {'rna2p': 4, 'rna3p': 23} Time building chain proxies: 7.70, per 1000 atoms: 0.70 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: 2.83 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.43 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: 6.08 Time building geometry restraints manager: 3.25 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: 15265 1.88 - 3.76: 329 3.76 - 5.65: 41 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 - 30.15: 6624 30.15 - 60.30: 281 60.30 - 90.45: 65 90.45 - 120.60: 0 120.60 - 150.75: 1 Dihedral angle restraints: 6971 sinusoidal: 3526 harmonic: 3445 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 200.00 49.25 150.75 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" CA ILE A 734 " pdb=" C ILE A 734 " pdb=" N ASN A 735 " pdb=" CA ASN A 735 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA TYR A1139 " pdb=" C TYR A1139 " pdb=" N ARG A1140 " pdb=" CA ARG A1140 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 6968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1379 0.049 - 0.098: 310 0.098 - 0.147: 63 0.147 - 0.196: 5 0.196 - 0.245: 1 Chirality restraints: 1758 Sorted by residual: chirality pdb=" CB THR A 562 " pdb=" CA THR A 562 " pdb=" OG1 THR A 562 " pdb=" CG2 THR A 562 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB THR A 628 " pdb=" CA THR A 628 " pdb=" OG1 THR A 628 " pdb=" CG2 THR A 628 " both_signs ideal model delta sigma weight residual False 2.55 2.74 -0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CB THR A 239 " pdb=" CA THR A 239 " pdb=" OG1 THR A 239 " pdb=" CG2 THR A 239 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.810 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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= 0.310 Angle : 0.697 9.410 15649 Z= 0.394 Chirality : 0.043 0.245 1758 Planarity : 0.004 0.044 1759 Dihedral : 16.395 150.753 4745 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.37 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 (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: -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 TRP 0.017 0.002 TRP A 888 HIS 0.006 0.001 HIS A 766 PHE 0.027 0.002 PHE A 806 TYR 0.024 0.002 TYR A 157 ARG 0.009 0.001 ARG A 928 *********************** 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 : 1.203 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: 1.6911 time to fit residues: 189.4901 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 : 1.240 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11371 Z= 0.393 Angle : 0.613 10.288 15649 Z= 0.327 Chirality : 0.042 0.164 1758 Planarity : 0.004 0.042 1759 Dihedral : 16.103 144.869 2317 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.05 % Allowed : 6.85 % Favored : 92.10 % 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: -0.69 (0.24), residues: 1158 helix: 0.24 (0.20), residues: 605 sheet: -1.25 (0.45), residues: 132 loop : -1.05 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 888 HIS 0.004 0.001 HIS A1219 PHE 0.016 0.002 PHE A 757 TYR 0.021 0.002 TYR A 544 ARG 0.007 0.001 ARG A 307 *********************** 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 63 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 1.294 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 1.3400 time to fit residues: 82.4389 Evaluate side-chains 39 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 442 ASN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11371 Z= 0.155 Angle : 0.494 8.526 15649 Z= 0.261 Chirality : 0.037 0.148 1758 Planarity : 0.003 0.039 1759 Dihedral : 15.886 147.702 2315 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.05 % Allowed : 8.47 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1158 helix: 0.81 (0.21), residues: 608 sheet: -1.14 (0.46), residues: 131 loop : -0.80 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 888 HIS 0.008 0.001 HIS A 587 PHE 0.013 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 *********************** 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 59 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.322 Fit side-chains outliers start: 11 outliers final: 2 residues processed: 52 average time/residue: 1.2839 time to fit residues: 73.6191 Evaluate side-chains 34 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11371 Z= 0.214 Angle : 0.489 7.374 15649 Z= 0.259 Chirality : 0.038 0.149 1758 Planarity : 0.003 0.038 1759 Dihedral : 15.776 147.279 2315 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.14 % Allowed : 9.51 % Favored : 89.34 % 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: 0.25 (0.25), residues: 1158 helix: 1.11 (0.21), residues: 607 sheet: -1.07 (0.46), residues: 131 loop : -0.71 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 888 HIS 0.003 0.001 HIS A 956 PHE 0.015 0.001 PHE A 180 TYR 0.018 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 *********************** 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 52 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 1.178 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 1.1332 time to fit residues: 55.9168 Evaluate side-chains 40 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 66 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 HIS A1211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 11371 Z= 0.485 Angle : 0.610 6.738 15649 Z= 0.322 Chirality : 0.044 0.171 1758 Planarity : 0.003 0.049 1759 Dihedral : 15.744 144.867 2315 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.24 % Allowed : 10.47 % Favored : 88.30 % 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: 0.06 (0.25), residues: 1158 helix: 0.99 (0.21), residues: 606 sheet: -1.29 (0.45), residues: 132 loop : -0.80 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 385 HIS 0.010 0.001 HIS A 587 PHE 0.018 0.002 PHE A 757 TYR 0.022 0.002 TYR A 544 ARG 0.007 0.000 ARG A 307 *********************** 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 44 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 1.169 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 38 average time/residue: 1.0380 time to fit residues: 44.9886 Evaluate side-chains 39 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 644 THR Chi-restraints excluded: chain A residue 659 LYS Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 1077 ASP Chi-restraints excluded: chain A residue 1167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11371 Z= 0.175 Angle : 0.477 7.703 15649 Z= 0.252 Chirality : 0.038 0.149 1758 Planarity : 0.003 0.043 1759 Dihedral : 15.769 147.864 2315 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.43 % Allowed : 10.28 % Favored : 88.30 % 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: 0.42 (0.25), residues: 1158 helix: 1.28 (0.21), residues: 608 sheet: -1.17 (0.46), residues: 131 loop : -0.61 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 888 HIS 0.007 0.001 HIS A 587 PHE 0.013 0.001 PHE A 180 TYR 0.017 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 *********************** 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: 15 poor density : 40 time to evaluate : 1.158 Fit side-chains REVERT: A 483 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7652 (p0) outliers start: 15 outliers final: 7 residues processed: 49 average time/residue: 1.0605 time to fit residues: 58.4689 Evaluate side-chains 36 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 628 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11371 Z= 0.235 Angle : 0.493 10.098 15649 Z= 0.259 Chirality : 0.038 0.152 1758 Planarity : 0.003 0.044 1759 Dihedral : 15.719 147.104 2315 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.24 % Allowed : 11.04 % Favored : 87.73 % 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: 0.49 (0.26), residues: 1158 helix: 1.34 (0.21), residues: 608 sheet: -1.20 (0.45), residues: 131 loop : -0.57 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 385 HIS 0.006 0.001 HIS A 587 PHE 0.014 0.001 PHE A 180 TYR 0.018 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 *********************** 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 44 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 1.205 Fit side-chains REVERT: A 483 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (p0) outliers start: 13 outliers final: 7 residues processed: 39 average time/residue: 0.8417 time to fit residues: 38.6252 Evaluate side-chains 39 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 628 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2590 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= 0.268 Angle : 0.511 12.085 15649 Z= 0.266 Chirality : 0.039 0.153 1758 Planarity : 0.003 0.046 1759 Dihedral : 15.707 146.450 2315 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.95 % Allowed : 11.32 % Favored : 87.73 % 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: 0.48 (0.25), residues: 1158 helix: 1.34 (0.21), residues: 608 sheet: -1.21 (0.45), residues: 131 loop : -0.59 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 655 HIS 0.004 0.001 HIS A 587 PHE 0.014 0.001 PHE A 180 TYR 0.019 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 *********************** 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 45 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 1.187 Fit side-chains REVERT: A 483 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7660 (p0) outliers start: 10 outliers final: 8 residues processed: 41 average time/residue: 1.0456 time to fit residues: 48.8850 Evaluate side-chains 39 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 483 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 628 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11371 Z= 0.269 Angle : 0.523 12.815 15649 Z= 0.271 Chirality : 0.039 0.153 1758 Planarity : 0.003 0.046 1759 Dihedral : 15.707 146.616 2315 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.95 % Allowed : 11.89 % Favored : 87.16 % 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: 0.49 (0.25), residues: 1158 helix: 1.35 (0.21), residues: 608 sheet: -1.25 (0.44), residues: 131 loop : -0.56 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 655 HIS 0.003 0.001 HIS A 587 PHE 0.014 0.001 PHE A 180 TYR 0.018 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 *********************** 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 43 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 1.337 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 1.0081 time to fit residues: 45.0825 Evaluate side-chains 38 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 628 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2680 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= 0.207 Angle : 0.508 13.172 15649 Z= 0.261 Chirality : 0.038 0.148 1758 Planarity : 0.003 0.043 1759 Dihedral : 15.701 147.536 2315 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.01 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 (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: 0.58 (0.25), residues: 1158 helix: 1.42 (0.21), residues: 609 sheet: -1.19 (0.45), residues: 130 loop : -0.53 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 385 HIS 0.006 0.001 HIS A 587 PHE 0.014 0.001 PHE A 180 TYR 0.017 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 ********************** 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 40 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 1.308 Fit side-chains outliers start: 8 outliers final: 9 residues processed: 38 average time/residue: 0.8731 time to fit residues: 38.8973 Evaluate side-chains 39 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 462 VAL Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 628 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 0.0030 chunk 40 optimal weight: 0.3980 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3327 r_free = 0.3327 target = 0.081133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067281 restraints weight = 26631.998| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.73 r_work: 0.2912 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11371 Z= 0.143 Angle : 0.480 13.168 15649 Z= 0.245 Chirality : 0.037 0.139 1758 Planarity : 0.003 0.039 1759 Dihedral : 15.671 149.383 2315 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.67 % Allowed : 12.08 % 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 (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: 0.74 (0.26), residues: 1158 helix: 1.57 (0.21), residues: 609 sheet: -1.10 (0.45), residues: 130 loop : -0.51 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 888 HIS 0.006 0.001 HIS A 485 PHE 0.012 0.001 PHE A 180 TYR 0.015 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2495.26 seconds wall clock time: 46 minutes 35.43 seconds (2795.43 seconds total)