Starting phenix.real_space_refine on Mon Dec 30 22:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yna_33956/12_2024/7yna_33956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yna_33956/12_2024/7yna_33956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/12_2024/7yna_33956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yna_33956/12_2024/7yna_33956.map" model { file = "/net/cci-nas-00/data/ceres_data/7yna_33956/12_2024/7yna_33956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yna_33956/12_2024/7yna_33956.cif" } resolution = 3.64 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= 0.003 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 63 5.49 5 S 57 5.16 5 C 8468 2.51 5 N 2454 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13784 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1536, 12447 Classifications: {'peptide': 1536} Link IDs: {'PTRANS': 84, 'TRANS': 1451} Chain breaks: 4 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 17} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 527 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 10, 'rna3p_pyr': 12} Link IDs: {'rna2p': 3, 'rna3p': 21} Time building chain proxies: 8.61, per 1000 atoms: 0.62 Number of scatterers: 13784 At special positions: 0 Unit cell: (92.02, 171.2, 132.68, 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 57 16.00 P 63 15.00 O 2742 8.00 N 2454 7.00 C 8468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2858 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 22.2% alpha, 15.3% beta 16 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 58 through 74 removed outlier: 3.510A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 291 through 295 removed outlier: 4.037A pdb=" N ARG A 294 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.945A pdb=" N LEU A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 365 removed outlier: 4.080A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.613A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.562A pdb=" N ASN A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.651A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 787 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.650A pdb=" N GLY A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.986A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 962 " --> pdb=" O TYR A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1109 removed outlier: 4.178A pdb=" N GLU A1106 " --> pdb=" O ASN A1102 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS A1107 " --> pdb=" O PHE A1103 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1108 " --> pdb=" O ASP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1246 removed outlier: 3.980A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1265 Processing helix chain 'A' and resid 1300 through 1305 removed outlier: 4.132A pdb=" N MET A1305 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1427 removed outlier: 3.975A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1476 removed outlier: 3.646A pdb=" N GLN A1476 " --> pdb=" O ILE A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 Processing helix chain 'A' and resid 1538 through 1548 Processing helix chain 'A' and resid 1565 through 1569 removed outlier: 4.032A pdb=" N ASP A1568 " --> pdb=" O ARG A1565 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A1569 " --> pdb=" O LYS A1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1565 through 1569' Processing helix chain 'A' and resid 1575 through 1580 Processing helix chain 'A' and resid 1588 through 1595 removed outlier: 3.569A pdb=" N THR A1594 " --> pdb=" O GLN A1590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.709A pdb=" N MET A 17 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 190 " --> pdb=" O MET A 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 171 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 removed outlier: 3.630A pdb=" N TYR A 577 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.742A pdb=" N GLU A 497 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 723 through 724 removed outlier: 3.743A pdb=" N VAL A 630 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 660 removed outlier: 3.518A pdb=" N LEU A 728 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.594A pdb=" N PHE A 757 " --> pdb=" O HIS A 741 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 removed outlier: 3.603A pdb=" N SER A1363 " --> pdb=" O SER A1455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 993 removed outlier: 4.035A pdb=" N VAL A1275 " --> pdb=" O GLY A 993 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1001 through 1011 removed outlier: 8.390A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 19.405A pdb=" N CYS A1143 " --> pdb=" O LYS A1223 " (cutoff:3.500A) removed outlier: 14.370A pdb=" N LYS A1223 " --> pdb=" O CYS A1143 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N GLU A1145 " --> pdb=" O ASP A1221 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP A1221 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE A1220 " --> pdb=" O GLU A1007 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU A1007 " --> pdb=" O PHE A1220 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1222 " --> pdb=" O PHE A1005 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A1005 " --> pdb=" O LEU A1222 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLU A1224 " --> pdb=" O GLN A1003 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLN A1003 " --> pdb=" O GLU A1224 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N GLU A1226 " --> pdb=" O HIS A1001 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N HIS A1001 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1044 through 1047 Processing sheet with id=AB8, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1086 removed outlier: 3.670A pdb=" N LEU A1096 " --> pdb=" O PHE A1083 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1085 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202 Processing sheet with id=AC2, first strand: chain 'A' and resid 1385 through 1387 307 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 4.12 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: 3596 1.33 - 1.45: 2944 1.45 - 1.57: 7491 1.57 - 1.69: 124 1.69 - 1.81: 82 Bond restraints: 14237 Sorted by residual: bond pdb=" C CYS A1560 " pdb=" N TYR A1561 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.42e+00 bond pdb=" N CYS A 965 " pdb=" CA CYS A 965 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 7.06e+00 bond pdb=" N CYS A 706 " pdb=" CA CYS A 706 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" N CYS A 711 " pdb=" CA CYS A 711 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.68e+00 bond pdb=" N CYS A 708 " pdb=" CA CYS A 708 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.25e-02 6.40e+03 6.19e+00 ... (remaining 14232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19113 2.23 - 4.45: 342 4.45 - 6.68: 25 6.68 - 8.91: 3 8.91 - 11.13: 1 Bond angle restraints: 19484 Sorted by residual: angle pdb=" N SER A1080 " pdb=" CA SER A1080 " pdb=" C SER A1080 " ideal model delta sigma weight residual 108.34 113.35 -5.01 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N LYS A1586 " pdb=" CA LYS A1586 " pdb=" C LYS A1586 " ideal model delta sigma weight residual 114.75 110.41 4.34 1.26e+00 6.30e-01 1.18e+01 angle pdb=" CA CYS A 708 " pdb=" C CYS A 708 " pdb=" O CYS A 708 " ideal model delta sigma weight residual 121.55 118.02 3.53 1.06e+00 8.90e-01 1.11e+01 angle pdb=" N GLN A 884 " pdb=" CA GLN A 884 " pdb=" C GLN A 884 " ideal model delta sigma weight residual 110.80 103.99 6.81 2.13e+00 2.20e-01 1.02e+01 angle pdb=" C SER A1403 " pdb=" N ASP A1404 " pdb=" CA ASP A1404 " ideal model delta sigma weight residual 121.54 115.60 5.94 1.91e+00 2.74e-01 9.69e+00 ... (remaining 19479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 8376 34.14 - 68.28: 289 68.28 - 102.42: 35 102.42 - 136.56: 2 136.56 - 170.70: 1 Dihedral angle restraints: 8703 sinusoidal: 4272 harmonic: 4431 Sorted by residual: dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 173 " pdb=" C LEU A 173 " pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' U B -14 " pdb=" C3' U B -14 " pdb=" O3' U B -14 " pdb=" P G B -13 " ideal model delta sinusoidal sigma weight residual -110.00 60.70 -170.70 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1524 0.048 - 0.097: 440 0.097 - 0.145: 103 0.145 - 0.193: 13 0.193 - 0.241: 4 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C3' U B -14 " pdb=" C4' U B -14 " pdb=" O3' U B -14 " pdb=" C2' U B -14 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1' A B 13 " pdb=" O4' A B 13 " pdb=" C2' A B 13 " pdb=" N9 A B 13 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA CYS A1342 " pdb=" N CYS A1342 " pdb=" C CYS A1342 " pdb=" CB CYS A1342 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2081 not shown) Planarity restraints: 2315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " -0.052 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO A 864 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.037 2.00e-02 2.50e+03 1.69e-02 8.56e+00 pdb=" N9 G B 9 " 0.043 2.00e-02 2.50e+03 pdb=" C8 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G B 9 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 9 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G B 9 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 9 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1311 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C PRO A1311 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO A1311 " -0.017 2.00e-02 2.50e+03 pdb=" N CYS A1312 " -0.015 2.00e-02 2.50e+03 ... (remaining 2312 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 609 2.69 - 3.25: 13133 3.25 - 3.80: 20329 3.80 - 4.35: 25821 4.35 - 4.90: 44074 Nonbonded interactions: 103966 Sorted by model distance: nonbonded pdb=" O2' A B 11 " pdb=" O4' C B 12 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 445 " pdb=" OP1 A B -2 " model vdw 2.186 3.040 nonbonded pdb=" NZ LYS A1004 " pdb=" O PHE A1005 " model vdw 2.229 3.120 nonbonded pdb=" NE2 HIS A 931 " pdb=" OG1 THR A1444 " model vdw 2.241 3.120 nonbonded pdb=" NH1 ARG A 974 " pdb=" O ASP A1298 " model vdw 2.241 3.120 ... (remaining 103961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.410 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 : 0.007 0.064 14237 Z= 0.429 Angle : 0.729 11.132 19484 Z= 0.406 Chirality : 0.048 0.241 2084 Planarity : 0.005 0.079 2315 Dihedral : 16.960 170.704 5845 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.06 % Favored : 83.81 % Rotamer: Outliers : 0.60 % Allowed : 7.22 % Favored : 92.19 % 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: -4.75 (0.17), residues: 1526 helix: -1.14 (0.28), residues: 300 sheet: -3.22 (0.26), residues: 281 loop : -4.07 (0.15), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1600 HIS 0.005 0.002 HIS A1473 PHE 0.015 0.002 PHE A 528 TYR 0.021 0.002 TYR A 863 ARG 0.005 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.677 Fit side-chains REVERT: A 311 ASP cc_start: 0.8125 (t0) cc_final: 0.7676 (t70) REVERT: A 1065 ARG cc_start: 0.8012 (mmm160) cc_final: 0.7252 (ttm170) REVERT: A 1211 MET cc_start: 0.7960 (tmm) cc_final: 0.7123 (tmm) REVERT: A 1270 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7339 (mttm) REVERT: A 1342 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7846 (p) outliers start: 8 outliers final: 3 residues processed: 74 average time/residue: 0.3636 time to fit residues: 37.7740 Evaluate side-chains 48 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 708 CYS Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1342 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 306 HIS A 456 GLN A 586 ASN A1095 HIS A1136 ASN A1207 ASN A1417 HIS A1419 HIS A1452 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14237 Z= 0.167 Angle : 0.606 12.166 19484 Z= 0.315 Chirality : 0.043 0.209 2084 Planarity : 0.005 0.063 2315 Dihedral : 16.262 164.829 2639 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.37 % Allowed : 10.04 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.19), residues: 1526 helix: 0.28 (0.31), residues: 311 sheet: -2.47 (0.28), residues: 275 loop : -3.72 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.011 0.001 PHE A 15 TYR 0.011 0.001 TYR A1081 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.586 Fit side-chains REVERT: A 305 ASP cc_start: 0.7252 (t0) cc_final: 0.6802 (t0) REVERT: A 410 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7759 (pp) REVERT: A 1065 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7198 (ttm170) REVERT: A 1211 MET cc_start: 0.7918 (tmm) cc_final: 0.7220 (tmm) REVERT: A 1270 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7334 (mttm) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.3433 time to fit residues: 35.7995 Evaluate side-chains 56 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.0370 chunk 119 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 115 optimal weight: 7.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1105 GLN A1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14237 Z= 0.175 Angle : 0.566 12.426 19484 Z= 0.293 Chirality : 0.042 0.206 2084 Planarity : 0.005 0.057 2315 Dihedral : 16.115 165.090 2637 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 0.82 % Allowed : 11.98 % Favored : 87.20 % 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: -3.24 (0.20), residues: 1526 helix: 0.79 (0.31), residues: 312 sheet: -2.10 (0.29), residues: 276 loop : -3.44 (0.16), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.011 0.001 PHE A 776 TYR 0.012 0.001 TYR A 492 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 1.677 Fit side-chains REVERT: A 410 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7876 (pt) REVERT: A 1065 ARG cc_start: 0.7866 (mmm160) cc_final: 0.7112 (ttm170) REVERT: A 1211 MET cc_start: 0.7901 (tmm) cc_final: 0.7482 (tmm) REVERT: A 1270 LYS cc_start: 0.7602 (mmmt) cc_final: 0.7309 (mttm) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.3254 time to fit residues: 31.0526 Evaluate side-chains 57 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14237 Z= 0.176 Angle : 0.555 12.438 19484 Z= 0.284 Chirality : 0.042 0.205 2084 Planarity : 0.004 0.055 2315 Dihedral : 16.002 164.405 2637 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 1.64 % Allowed : 13.39 % Favored : 84.97 % 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: -2.89 (0.20), residues: 1526 helix: 1.19 (0.32), residues: 312 sheet: -1.83 (0.29), residues: 291 loop : -3.28 (0.17), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.010 0.001 PHE A 776 TYR 0.010 0.001 TYR A 863 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 1.580 Fit side-chains REVERT: A 410 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7888 (pt) REVERT: A 1065 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7171 (ttp-170) REVERT: A 1211 MET cc_start: 0.7899 (tmm) cc_final: 0.7264 (tmm) REVERT: A 1270 LYS cc_start: 0.7568 (mmmt) cc_final: 0.7339 (mttm) outliers start: 22 outliers final: 16 residues processed: 68 average time/residue: 0.3094 time to fit residues: 31.4188 Evaluate side-chains 63 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1479 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 8.9990 chunk 86 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.212 Angle : 0.566 12.055 19484 Z= 0.289 Chirality : 0.042 0.212 2084 Planarity : 0.004 0.056 2315 Dihedral : 15.957 164.844 2637 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer: Outliers : 1.86 % Allowed : 14.43 % Favored : 83.71 % 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: -2.70 (0.20), residues: 1526 helix: 1.34 (0.32), residues: 310 sheet: -1.66 (0.29), residues: 291 loop : -3.17 (0.17), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.012 0.001 PHE A 776 TYR 0.015 0.001 TYR A 492 ARG 0.005 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 1.602 Fit side-chains REVERT: A 410 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7443 (pp) REVERT: A 1065 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7187 (ttm170) REVERT: A 1211 MET cc_start: 0.7924 (tmm) cc_final: 0.7266 (tmm) outliers start: 25 outliers final: 18 residues processed: 68 average time/residue: 0.2693 time to fit residues: 28.5739 Evaluate side-chains 66 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 152 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14237 Z= 0.136 Angle : 0.527 12.527 19484 Z= 0.269 Chirality : 0.040 0.190 2084 Planarity : 0.004 0.050 2315 Dihedral : 15.894 163.333 2637 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.56 % Allowed : 14.88 % Favored : 83.56 % 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: -2.34 (0.21), residues: 1526 helix: 1.64 (0.32), residues: 310 sheet: -1.27 (0.30), residues: 274 loop : -2.97 (0.17), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.009 0.001 PHE A1407 TYR 0.008 0.001 TYR A 313 ARG 0.006 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 1.593 Fit side-chains REVERT: A 1065 ARG cc_start: 0.7781 (mmm160) cc_final: 0.7150 (ttp-170) REVERT: A 1211 MET cc_start: 0.7836 (tmm) cc_final: 0.7346 (tmm) outliers start: 21 outliers final: 17 residues processed: 68 average time/residue: 0.2616 time to fit residues: 28.0517 Evaluate side-chains 62 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1491 MET Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.210 Angle : 0.557 11.988 19484 Z= 0.284 Chirality : 0.042 0.210 2084 Planarity : 0.004 0.051 2315 Dihedral : 15.834 164.602 2636 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 1.86 % Allowed : 15.10 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.21), residues: 1526 helix: 1.70 (0.32), residues: 309 sheet: -1.18 (0.30), residues: 281 loop : -2.96 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.021 0.001 PHE A1527 TYR 0.011 0.001 TYR A 492 ARG 0.004 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 1065 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7176 (ttm170) REVERT: A 1211 MET cc_start: 0.7878 (tmm) cc_final: 0.7312 (tmm) outliers start: 25 outliers final: 18 residues processed: 65 average time/residue: 0.2727 time to fit residues: 27.7132 Evaluate side-chains 61 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.0670 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.210 Angle : 0.559 11.848 19484 Z= 0.286 Chirality : 0.042 0.210 2084 Planarity : 0.004 0.054 2315 Dihedral : 15.826 164.864 2636 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 1.64 % Allowed : 15.77 % Favored : 82.59 % 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: -2.22 (0.21), residues: 1526 helix: 1.74 (0.32), residues: 308 sheet: -1.16 (0.31), residues: 279 loop : -2.90 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.018 0.001 PHE A1527 TYR 0.011 0.001 TYR A 863 ARG 0.006 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 46 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: A 1065 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7160 (ttp-170) REVERT: A 1211 MET cc_start: 0.7866 (tmm) cc_final: 0.7288 (tmm) outliers start: 22 outliers final: 19 residues processed: 66 average time/residue: 0.3188 time to fit residues: 31.8726 Evaluate side-chains 62 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14237 Z= 0.217 Angle : 0.571 11.620 19484 Z= 0.290 Chirality : 0.042 0.210 2084 Planarity : 0.004 0.052 2315 Dihedral : 15.811 164.858 2636 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 1.64 % Allowed : 16.15 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1526 helix: 1.76 (0.32), residues: 308 sheet: -1.35 (0.30), residues: 290 loop : -2.84 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 PHE 0.015 0.001 PHE A1527 TYR 0.011 0.001 TYR A 863 ARG 0.006 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 1.686 Fit side-chains revert: symmetry clash REVERT: A 1065 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7189 (ttm170) REVERT: A 1211 MET cc_start: 0.7869 (tmm) cc_final: 0.7439 (tmm) REVERT: A 1533 TRP cc_start: 0.8123 (OUTLIER) cc_final: 0.7705 (m-10) outliers start: 22 outliers final: 19 residues processed: 63 average time/residue: 0.2889 time to fit residues: 28.4356 Evaluate side-chains 63 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 133 optimal weight: 0.0570 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14237 Z= 0.236 Angle : 0.577 11.270 19484 Z= 0.295 Chirality : 0.043 0.214 2084 Planarity : 0.005 0.055 2315 Dihedral : 15.816 165.143 2636 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 1.49 % Allowed : 16.29 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.21), residues: 1526 helix: 1.74 (0.32), residues: 308 sheet: -1.10 (0.31), residues: 272 loop : -2.88 (0.18), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.014 0.001 PHE A 528 TYR 0.012 0.001 TYR A 863 ARG 0.003 0.000 ARG A 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3052 Ramachandran restraints generated. 1526 Oldfield, 0 Emsley, 1526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 1065 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7111 (ttp-170) REVERT: A 1211 MET cc_start: 0.7881 (tmm) cc_final: 0.7432 (tmm) REVERT: A 1533 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.7674 (m-10) outliers start: 20 outliers final: 19 residues processed: 62 average time/residue: 0.2795 time to fit residues: 27.1906 Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063659 restraints weight = 36164.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065692 restraints weight = 19779.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.066981 restraints weight = 13757.542| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14237 Z= 0.151 Angle : 0.544 11.866 19484 Z= 0.275 Chirality : 0.041 0.195 2084 Planarity : 0.004 0.050 2315 Dihedral : 15.781 163.756 2636 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 1.56 % Allowed : 16.44 % Favored : 81.99 % 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: -2.00 (0.21), residues: 1526 helix: 1.76 (0.32), residues: 316 sheet: -1.00 (0.31), residues: 275 loop : -2.74 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 42 HIS 0.004 0.001 HIS A1473 PHE 0.014 0.001 PHE A1527 TYR 0.009 0.001 TYR A 313 ARG 0.003 0.000 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.64 seconds wall clock time: 42 minutes 35.68 seconds (2555.68 seconds total)