Starting phenix.real_space_refine on Thu Jun 12 17:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yna_33956/06_2025/7yna_33956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yna_33956/06_2025/7yna_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_33956/06_2025/7yna_33956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yna_33956/06_2025/7yna_33956.map" model { file = "/net/cci-nas-00/data/ceres_data/7yna_33956/06_2025/7yna_33956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yna_33956/06_2025/7yna_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.67, per 1000 atoms: 0.63 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: 3.46 Conformation dependent library (CDL) restraints added in 1.4 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: 4.65 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: 6.29 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: 2.180 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: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.900 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- 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= 0.293 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 Details of bonding type rmsd hydrogen bonds : bond 0.21404 ( 342) hydrogen bonds : angle 6.95324 ( 905) covalent geometry : bond 0.00655 (14237) covalent geometry : angle 0.72934 (19484) *********************** 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 : 1.376 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: 0.3508 time to fit residues: 36.3267 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 : 1.370 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061920 restraints weight = 36282.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.063943 restraints weight = 19843.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065202 restraints weight = 13895.748| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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= 0.122 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 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 342) hydrogen bonds : angle 4.70824 ( 905) covalent geometry : bond 0.00256 (14237) covalent geometry : angle 0.60609 (19484) *********************** 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 : 1.426 Fit side-chains REVERT: A 305 ASP cc_start: 0.7357 (t0) cc_final: 0.6801 (t0) REVERT: A 410 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7724 (pp) REVERT: A 585 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7841 (tp30) REVERT: A 989 ASP cc_start: 0.8167 (t70) cc_final: 0.7937 (t0) REVERT: A 1065 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7199 (ttm170) REVERT: A 1211 MET cc_start: 0.7933 (tmm) cc_final: 0.7198 (tmm) REVERT: A 1270 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7307 (mttm) outliers start: 5 outliers final: 3 residues processed: 71 average time/residue: 0.3087 time to fit residues: 32.3700 Evaluate side-chains 58 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 27 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 100 optimal weight: 0.2980 chunk 8 optimal weight: 0.0670 chunk 152 optimal weight: 6.9990 chunk 108 optimal weight: 0.0010 chunk 98 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A1246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.064807 restraints weight = 36581.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066967 restraints weight = 19012.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.068360 restraints weight = 12939.577| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1854 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= 0.099 Angle : 0.534 13.184 19484 Z= 0.275 Chirality : 0.041 0.186 2084 Planarity : 0.004 0.050 2315 Dihedral : 16.058 164.180 2637 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 0.97 % Allowed : 11.98 % Favored : 87.05 % 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: -2.94 (0.20), residues: 1526 helix: 1.03 (0.32), residues: 312 sheet: -1.70 (0.30), residues: 266 loop : -3.30 (0.16), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 42 HIS 0.006 0.001 HIS A1473 PHE 0.011 0.001 PHE A1407 TYR 0.014 0.001 TYR A 492 ARG 0.005 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 342) hydrogen bonds : angle 3.89627 ( 905) covalent geometry : bond 0.00210 (14237) covalent geometry : angle 0.53440 (19484) *********************** 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 76 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 2.310 Fit side-chains REVERT: A 60 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8646 (tp) REVERT: A 1065 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7116 (ttp-170) REVERT: A 1211 MET cc_start: 0.7876 (tmm) cc_final: 0.7469 (tmm) REVERT: A 1270 LYS cc_start: 0.7587 (mmmt) cc_final: 0.7267 (mttm) outliers start: 13 outliers final: 8 residues processed: 75 average time/residue: 0.3300 time to fit residues: 36.2735 Evaluate side-chains 57 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 731 GLU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1087 THR 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 115 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN A 865 HIS A1105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.081038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.060779 restraints weight = 36928.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062845 restraints weight = 19969.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.064141 restraints weight = 13912.344| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14237 Z= 0.184 Angle : 0.603 12.207 19484 Z= 0.310 Chirality : 0.044 0.226 2084 Planarity : 0.005 0.062 2315 Dihedral : 15.976 165.502 2637 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 1.64 % Allowed : 13.62 % Favored : 84.75 % 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: -2.88 (0.20), residues: 1526 helix: 1.15 (0.32), residues: 310 sheet: -1.65 (0.29), residues: 283 loop : -3.31 (0.17), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1600 HIS 0.008 0.001 HIS A 306 PHE 0.017 0.002 PHE A 528 TYR 0.017 0.001 TYR A 863 ARG 0.004 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 342) hydrogen bonds : angle 4.13472 ( 905) covalent geometry : bond 0.00424 (14237) covalent geometry : angle 0.60275 (19484) *********************** 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 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 1.514 Fit side-chains REVERT: A 1065 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7188 (ttm170) REVERT: A 1211 MET cc_start: 0.7970 (tmm) cc_final: 0.7310 (tmm) REVERT: A 1270 LYS cc_start: 0.7621 (mmmt) cc_final: 0.7368 (mttm) outliers start: 22 outliers final: 17 residues processed: 68 average time/residue: 0.3108 time to fit residues: 31.4742 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 : 1.522 ------------------------------------------------------------------------------- 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 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 729 VAL 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 1479 LYS Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 82 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A1483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.080266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.059992 restraints weight = 37491.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.061986 restraints weight = 20572.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.063244 restraints weight = 14534.236| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14237 Z= 0.213 Angle : 0.621 11.343 19484 Z= 0.321 Chirality : 0.045 0.227 2084 Planarity : 0.005 0.068 2315 Dihedral : 16.001 165.957 2637 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 2.23 % Allowed : 14.96 % Favored : 82.81 % 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: -2.86 (0.20), residues: 1526 helix: 1.14 (0.31), residues: 309 sheet: -1.75 (0.29), residues: 290 loop : -3.25 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.013 0.002 PHE A 776 TYR 0.016 0.001 TYR A 863 ARG 0.005 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 342) hydrogen bonds : angle 4.22265 ( 905) covalent geometry : bond 0.00492 (14237) covalent geometry : angle 0.62138 (19484) *********************** 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 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 1.466 Fit side-chains REVERT: A 1065 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7208 (ttm170) REVERT: A 1211 MET cc_start: 0.7963 (tmm) cc_final: 0.7407 (tmm) REVERT: A 1270 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7343 (mttm) REVERT: A 1533 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7763 (m-10) outliers start: 30 outliers final: 19 residues processed: 70 average time/residue: 0.2764 time to fit residues: 30.1648 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 : 1.577 ------------------------------------------------------------------------------- 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 206 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 519 MET 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 1103 PHE Chi-restraints excluded: chain A residue 1156 VAL 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 1491 MET Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1533 TRP 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 71 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 142 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.081182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.060918 restraints weight = 37390.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.062957 restraints weight = 20458.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.064252 restraints weight = 14378.338| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14237 Z= 0.158 Angle : 0.589 11.343 19484 Z= 0.303 Chirality : 0.043 0.212 2084 Planarity : 0.005 0.062 2315 Dihedral : 15.958 165.244 2637 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.23 % Allowed : 15.70 % Favored : 82.07 % 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: -2.67 (0.20), residues: 1526 helix: 1.33 (0.31), residues: 309 sheet: -1.63 (0.29), residues: 291 loop : -3.13 (0.17), residues: 926 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 A1219 TYR 0.012 0.001 TYR A 863 ARG 0.005 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 342) hydrogen bonds : angle 4.06334 ( 905) covalent geometry : bond 0.00363 (14237) covalent geometry : angle 0.58904 (19484) *********************** 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 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 1.505 Fit side-chains REVERT: A 1065 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7210 (ttp-170) REVERT: A 1211 MET cc_start: 0.7949 (tmm) cc_final: 0.7414 (tmm) REVERT: A 1270 LYS cc_start: 0.7624 (mmmt) cc_final: 0.7351 (mttm) REVERT: A 1533 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7745 (m-10) outliers start: 30 outliers final: 20 residues processed: 70 average time/residue: 0.2751 time to fit residues: 29.8775 Evaluate side-chains 64 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL 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 519 MET 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 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 1305 MET 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 1500 VAL Chi-restraints excluded: chain A residue 1533 TRP 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 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.080342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.060064 restraints weight = 37431.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.062095 restraints weight = 20207.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.063398 restraints weight = 14119.461| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 14237 Z= 0.196 Angle : 0.621 11.701 19484 Z= 0.318 Chirality : 0.045 0.229 2084 Planarity : 0.005 0.066 2315 Dihedral : 15.944 165.786 2636 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.08 % Allowed : 16.22 % Favored : 81.70 % 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: -2.67 (0.20), residues: 1526 helix: 1.29 (0.31), residues: 309 sheet: -1.64 (0.30), residues: 289 loop : -3.11 (0.17), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 PHE 0.013 0.001 PHE A 776 TYR 0.015 0.001 TYR A 863 ARG 0.004 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 342) hydrogen bonds : angle 4.14514 ( 905) covalent geometry : bond 0.00451 (14237) covalent geometry : angle 0.62056 (19484) *********************** 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 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 1.575 Fit side-chains REVERT: A 1065 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7227 (ttm170) REVERT: A 1211 MET cc_start: 0.7962 (tmm) cc_final: 0.7393 (tmm) REVERT: A 1270 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7336 (mttm) REVERT: A 1283 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: A 1533 TRP cc_start: 0.8209 (OUTLIER) cc_final: 0.7784 (m-10) outliers start: 28 outliers final: 22 residues processed: 68 average time/residue: 0.2765 time to fit residues: 29.2229 Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL 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 519 MET 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 1283 TYR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1367 ASP 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 1500 VAL Chi-restraints excluded: chain A residue 1533 TRP 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 126 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.079438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.059123 restraints weight = 37406.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061150 restraints weight = 20308.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.062423 restraints weight = 14190.315| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14237 Z= 0.236 Angle : 0.651 10.898 19484 Z= 0.336 Chirality : 0.046 0.232 2084 Planarity : 0.005 0.066 2315 Dihedral : 15.985 166.455 2636 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 2.38 % Allowed : 16.29 % Favored : 81.32 % 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: -2.72 (0.20), residues: 1526 helix: 1.23 (0.31), residues: 308 sheet: -1.70 (0.30), residues: 291 loop : -3.12 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1600 HIS 0.006 0.001 HIS A1149 PHE 0.019 0.002 PHE A1219 TYR 0.016 0.001 TYR A 863 ARG 0.005 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 342) hydrogen bonds : angle 4.28217 ( 905) covalent geometry : bond 0.00545 (14237) covalent geometry : angle 0.65128 (19484) *********************** 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 75 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 43 time to evaluate : 1.521 Fit side-chains REVERT: A 366 MET cc_start: 0.6367 (ttm) cc_final: 0.6133 (mtt) REVERT: A 1065 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7298 (ttm170) REVERT: A 1211 MET cc_start: 0.8000 (tmm) cc_final: 0.7265 (tmm) REVERT: A 1270 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7372 (mttm) REVERT: A 1283 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7248 (m-10) REVERT: A 1473 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7951 (t-90) REVERT: A 1533 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7821 (m-10) outliers start: 32 outliers final: 24 residues processed: 71 average time/residue: 0.2810 time to fit residues: 31.1684 Evaluate side-chains 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 41 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 519 MET 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 1283 TYR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1473 HIS 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 1533 TRP 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 75 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.081471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.061252 restraints weight = 36702.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.063327 restraints weight = 19786.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.064648 restraints weight = 13788.852| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1807 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= 0.130 Angle : 0.581 11.625 19484 Z= 0.297 Chirality : 0.043 0.203 2084 Planarity : 0.005 0.063 2315 Dihedral : 15.909 164.812 2636 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 1.86 % Allowed : 17.11 % Favored : 81.03 % 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: -2.49 (0.21), residues: 1526 helix: 1.37 (0.31), residues: 316 sheet: -1.43 (0.30), residues: 282 loop : -3.02 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 42 HIS 0.005 0.001 HIS A1473 PHE 0.014 0.001 PHE A1219 TYR 0.011 0.001 TYR A 313 ARG 0.005 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 342) hydrogen bonds : angle 3.96926 ( 905) covalent geometry : bond 0.00295 (14237) covalent geometry : angle 0.58109 (19484) *********************** 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 71 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 1.411 Fit side-chains REVERT: A 473 MET cc_start: 0.8481 (mmm) cc_final: 0.8089 (mmm) REVERT: A 1065 ARG cc_start: 0.7877 (mmm160) cc_final: 0.7149 (ttp-170) REVERT: A 1211 MET cc_start: 0.8003 (tmm) cc_final: 0.7393 (tmm) REVERT: A 1270 LYS cc_start: 0.7637 (mmmt) cc_final: 0.7332 (mttm) REVERT: A 1473 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7951 (t-90) outliers start: 25 outliers final: 21 residues processed: 67 average time/residue: 0.2657 time to fit residues: 27.6186 Evaluate side-chains 66 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL 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 317 ILE Chi-restraints excluded: chain A residue 519 MET 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 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 1305 MET Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1473 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 128 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 104 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 141 optimal weight: 0.0770 chunk 121 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 152 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.065041 restraints weight = 36373.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.067096 restraints weight = 19836.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068409 restraints weight = 13770.186| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2307 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= 0.094 Angle : 0.536 12.333 19484 Z= 0.269 Chirality : 0.040 0.183 2084 Planarity : 0.004 0.060 2315 Dihedral : 15.821 162.404 2636 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 1.19 % Allowed : 17.71 % Favored : 81.10 % 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: -2.06 (0.21), residues: 1526 helix: 1.73 (0.32), residues: 316 sheet: -1.12 (0.32), residues: 265 loop : -2.74 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1509 HIS 0.004 0.001 HIS A1473 PHE 0.012 0.001 PHE A1407 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 342) hydrogen bonds : angle 3.59528 ( 905) covalent geometry : bond 0.00201 (14237) covalent geometry : angle 0.53571 (19484) ********************** 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 66 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 1065 ARG cc_start: 0.7763 (mmm160) cc_final: 0.7190 (ttp-170) REVERT: A 1211 MET cc_start: 0.7857 (tmm) cc_final: 0.7275 (tmm) REVERT: A 1270 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7382 (mttm) REVERT: A 1527 PHE cc_start: 0.8563 (t80) cc_final: 0.8246 (t80) outliers start: 16 outliers final: 13 residues processed: 62 average time/residue: 0.3271 time to fit residues: 31.5069 Evaluate side-chains 58 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 1.833 ------------------------------------------------------------------------------- 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 842 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 903 THR 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 1397 THR Chi-restraints excluded: chain A residue 1491 MET 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 157 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 865 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.059743 restraints weight = 37562.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061601 restraints weight = 21438.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.062780 restraints weight = 15473.491| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14237 Z= 0.250 Angle : 0.660 10.723 19484 Z= 0.339 Chirality : 0.046 0.237 2084 Planarity : 0.005 0.067 2315 Dihedral : 15.878 166.511 2636 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 1.56 % Allowed : 17.78 % Favored : 80.65 % 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: -2.39 (0.21), residues: 1526 helix: 1.37 (0.31), residues: 316 sheet: -1.50 (0.30), residues: 289 loop : -2.88 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 977 HIS 0.006 0.001 HIS A1149 PHE 0.017 0.002 PHE A1219 TYR 0.017 0.002 TYR A 863 ARG 0.008 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 342) hydrogen bonds : angle 4.17293 ( 905) covalent geometry : bond 0.00581 (14237) covalent geometry : angle 0.65983 (19484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3954.29 seconds wall clock time: 70 minutes 7.35 seconds (4207.35 seconds total)