Starting phenix.real_space_refine on Sat Sep 12 06:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yna_33956/09_2026/7yna_33956.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 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: {'RNAv2': 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: 3.00, per 1000 atoms: 0.22 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: 0.90 Conformation dependent library (CDL) restraints added in 465.0 milliseconds 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: 1.70 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: 2.93 Time building geometry restraints manager: 1.24 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: 18908 2.23 - 4.45: 508 4.45 - 6.68: 64 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=" C3' U B -14 " pdb=" O3' U B -14 " pdb=" P G B -13 " ideal model delta sigma weight residual 119.70 124.05 -4.35 1.20e+00 6.94e-01 1.31e+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=" O3' A B 5 " pdb=" C3' A B 5 " pdb=" C2' A B 5 " ideal model delta sigma weight residual 113.80 107.15 6.65 2.00e+00 2.50e-01 1.10e+01 ... (remaining 19479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.14: 8165 34.14 - 68.28: 301 68.28 - 102.42: 34 102.42 - 136.56: 0 136.56 - 170.70: 1 Dihedral angle restraints: 8501 sinusoidal: 4070 harmonic: 4431 Sorted by residual: dihedral pdb=" C4' A B 5 " pdb=" C3' A B 5 " pdb=" C2' A B 5 " pdb=" C1' A B 5 " ideal model delta sinusoidal sigma weight residual 36.34 -40.23 76.57 1 3.10e+00 1.04e-01 7.67e+02 dihedral pdb=" C4' A C 6 " pdb=" C3' A C 6 " pdb=" C2' A C 6 " pdb=" C1' A C 6 " ideal model delta sinusoidal sigma weight residual 36.34 -39.34 75.68 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' G B -13 " pdb=" C3' G B -13 " pdb=" C2' G B -13 " pdb=" C1' G B -13 " ideal model delta sinusoidal sigma weight residual 36.35 -38.88 75.23 1 3.10e+00 1.04e-01 7.44e+02 ... (remaining 8498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1702 0.071 - 0.141: 257 0.141 - 0.212: 35 0.212 - 0.282: 78 0.282 - 0.353: 12 Chirality restraints: 2084 Sorted by residual: chirality pdb=" C3' A B 5 " pdb=" C4' A B 5 " pdb=" O3' A B 5 " pdb=" C2' A B 5 " both_signs ideal model delta sigma weight residual False -2.50 -2.85 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C2' G B 9 " pdb=" C3' G B 9 " pdb=" O2' G B 9 " pdb=" C1' G B 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C3' A B -2 " pdb=" C4' A B -2 " pdb=" O3' A B -2 " pdb=" C2' A B -2 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.31e+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: 2.250 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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= 0.295 Angle : 0.824 11.132 19484 Z= 0.426 Chirality : 0.073 0.353 2084 Planarity : 0.005 0.079 2315 Dihedral : 17.177 170.704 5643 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.000 ARG A 444 TYR 0.021 0.002 TYR A 863 PHE 0.015 0.002 PHE A 528 TRP 0.015 0.002 TRP A1600 HIS 0.005 0.002 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.30 (14237) covalent geometry : angle 0.82357 / 0.43 (19484) hydrogen bonds : bond 0.21404 / 12.94 ( 342) hydrogen bonds : angle 6.95324 / 4.99 ( 905) *********************** 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 : 0.391 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: 0.7124 (tmm) REVERT: A 1270 LYS cc_start: 0.7649 (mmmt) cc_final: 0.7340 (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: 0.1315 time to fit residues: 13.8168 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 : 0.440 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3300 r_free = 0.3300 target = 0.082439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.062882 restraints weight = 36373.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.064881 restraints weight = 19965.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.066159 restraints weight = 13994.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066925 restraints weight = 11246.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.067483 restraints weight = 9866.091| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14237 Z= 0.170 Angle : 0.968 14.548 19484 Z= 0.433 Chirality : 0.093 1.086 2084 Planarity : 0.005 0.066 2315 Dihedral : 14.091 178.569 2437 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.37 % Allowed : 10.49 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.19), residues: 1526 helix: 0.20 (0.31), residues: 311 sheet: -2.51 (0.27), residues: 280 loop : -3.76 (0.16), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 62 TYR 0.011 0.001 TYR A 863 PHE 0.011 0.001 PHE A 776 TRP 0.020 0.001 TRP A 595 HIS 0.008 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (14237) covalent geometry : angle 0.96818 / 0.43 (19484) hydrogen bonds : bond 0.04928 / 3.05 ( 342) hydrogen bonds : angle 4.78239 / 3.40 ( 905) *********************** 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 67 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.513 Fit side-chains REVERT: A 97 ARG cc_start: 0.7516 (ptt90) cc_final: 0.7285 (ptt90) REVERT: A 305 ASP cc_start: 0.7272 (t0) cc_final: 0.6807 (t0) REVERT: A 410 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7775 (pp) REVERT: A 989 ASP cc_start: 0.8122 (t70) cc_final: 0.7911 (t0) REVERT: A 1065 ARG cc_start: 0.7834 (mmm160) cc_final: 0.7200 (ttm170) REVERT: A 1211 MET cc_start: 0.7990 (tmm) cc_final: 0.7222 (tmm) REVERT: A 1270 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7390 (mttm) outliers start: 5 outliers final: 3 residues processed: 67 average time/residue: 0.1335 time to fit residues: 12.9441 Evaluate side-chains 54 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 83 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 100 optimal weight: 0.4980 chunk 102 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A1246 ASN A1483 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.078705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.058848 restraints weight = 37818.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.060685 restraints weight = 21637.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.061847 restraints weight = 15649.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062586 restraints weight = 12856.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062994 restraints weight = 11378.898| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 14237 Z= 0.372 Angle : 0.990 11.287 19484 Z= 0.468 Chirality : 0.092 1.099 2084 Planarity : 0.006 0.084 2315 Dihedral : 14.456 177.916 2435 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 1.79 % Allowed : 14.36 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.19), residues: 1526 helix: 0.08 (0.30), residues: 316 sheet: -2.62 (0.27), residues: 280 loop : -3.73 (0.16), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 444 TYR 0.028 0.002 TYR A 863 PHE 0.020 0.002 PHE A1540 TRP 0.017 0.002 TRP A1597 HIS 0.007 0.002 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.37 (14237) covalent geometry : angle 0.99030 / 0.47 (19484) hydrogen bonds : bond 0.06396 / 4.08 ( 342) hydrogen bonds : angle 5.00213 / 3.56 ( 905) *********************** 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 67 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.558 Fit side-chains REVERT: A 60 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9241 (tt) REVERT: A 989 ASP cc_start: 0.8224 (t70) cc_final: 0.7906 (t0) REVERT: A 1065 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7231 (ttm170) REVERT: A 1211 MET cc_start: 0.8104 (tmm) cc_final: 0.7060 (tmm) REVERT: A 1270 LYS cc_start: 0.7702 (mmmt) cc_final: 0.7379 (mttm) REVERT: A 1533 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.8041 (m-10) outliers start: 24 outliers final: 16 residues processed: 66 average time/residue: 0.1262 time to fit residues: 12.7182 Evaluate side-chains 60 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 176 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 742 VAL 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 903 THR Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 1008 THR 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 1533 TRP Chi-restraints excluded: chain A residue 1600 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063818 restraints weight = 37031.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065942 restraints weight = 19549.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.067292 restraints weight = 13365.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068143 restraints weight = 10624.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.068623 restraints weight = 9204.280| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1778 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= 0.147 Angle : 0.773 11.684 19484 Z= 0.356 Chirality : 0.069 0.645 2084 Planarity : 0.005 0.064 2315 Dihedral : 14.290 175.904 2435 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.64 % Allowed : 15.85 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.20), residues: 1526 helix: 0.81 (0.31), residues: 310 sheet: -1.95 (0.29), residues: 283 loop : -3.43 (0.16), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.011 0.001 TYR A 313 PHE 0.011 0.001 PHE A 776 TRP 0.012 0.001 TRP A1600 HIS 0.004 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (14237) covalent geometry : angle 0.77313 / 0.36 (19484) hydrogen bonds : bond 0.04038 / 2.57 ( 342) hydrogen bonds : angle 4.24232 / 3.02 ( 905) *********************** 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 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.459 Fit side-chains REVERT: A 410 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7846 (pt) REVERT: A 989 ASP cc_start: 0.8223 (t70) cc_final: 0.7940 (t0) REVERT: A 1065 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7251 (ttm170) REVERT: A 1211 MET cc_start: 0.8029 (tmm) cc_final: 0.7153 (tmm) REVERT: A 1270 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7378 (mttm) outliers start: 22 outliers final: 12 residues processed: 72 average time/residue: 0.1187 time to fit residues: 13.1756 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 : 0.518 ------------------------------------------------------------------------------- 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 410 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE 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 67 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 152 optimal weight: 0.0670 chunk 150 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.064746 restraints weight = 36784.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.066893 restraints weight = 19751.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.068278 restraints weight = 13586.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.069139 restraints weight = 10811.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.069621 restraints weight = 9377.045| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2054 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= 0.129 Angle : 0.726 12.269 19484 Z= 0.333 Chirality : 0.064 0.663 2084 Planarity : 0.005 0.058 2315 Dihedral : 14.088 179.739 2435 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 2.31 % Allowed : 15.92 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.20), residues: 1526 helix: 1.21 (0.31), residues: 311 sheet: -1.72 (0.29), residues: 294 loop : -3.21 (0.17), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.010 0.001 TYR A 313 PHE 0.010 0.001 PHE A 747 TRP 0.010 0.001 TRP A1600 HIS 0.005 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (14237) covalent geometry : angle 0.72605 / 0.33 (19484) hydrogen bonds : bond 0.03662 / 2.32 ( 342) hydrogen bonds : angle 3.99403 / 2.84 ( 905) *********************** 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 84 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 0.545 Fit side-chains REVERT: A 410 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7908 (pt) REVERT: A 989 ASP cc_start: 0.8165 (t70) cc_final: 0.7932 (t0) REVERT: A 1065 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7263 (ttm170) REVERT: A 1211 MET cc_start: 0.7968 (tmm) cc_final: 0.7419 (tmm) REVERT: A 1270 LYS cc_start: 0.7631 (mmmt) cc_final: 0.7350 (mttm) REVERT: A 1444 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9198 (m) outliers start: 31 outliers final: 21 residues processed: 80 average time/residue: 0.1176 time to fit residues: 14.5332 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 228 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 648 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 861 VAL 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 1367 ASP Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 THR 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 7 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS 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 = 0.080345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.060622 restraints weight = 37370.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.062501 restraints weight = 21353.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063699 restraints weight = 15323.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064453 restraints weight = 12537.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.064897 restraints weight = 11076.742| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14237 Z= 0.290 Angle : 0.872 10.860 19484 Z= 0.408 Chirality : 0.078 0.754 2084 Planarity : 0.005 0.070 2315 Dihedral : 14.180 179.308 2434 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 2.68 % Allowed : 16.82 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.20), residues: 1526 helix: 0.92 (0.31), residues: 310 sheet: -1.61 (0.30), residues: 283 loop : -3.28 (0.17), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.021 0.002 TYR A 863 PHE 0.018 0.002 PHE A1540 TRP 0.014 0.002 TRP A1600 HIS 0.005 0.002 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (14237) covalent geometry : angle 0.87237 / 0.41 (19484) hydrogen bonds : bond 0.05309 / 3.42 ( 342) hydrogen bonds : angle 4.46330 / 3.17 ( 905) *********************** 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 80 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 44 time to evaluate : 0.529 Fit side-chains REVERT: A 73 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8659 (mp) REVERT: A 410 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 989 ASP cc_start: 0.8181 (t70) cc_final: 0.7876 (t0) REVERT: A 1065 ARG cc_start: 0.7939 (mmm160) cc_final: 0.7318 (ttm170) REVERT: A 1211 MET cc_start: 0.7975 (tmm) cc_final: 0.7476 (tmm) REVERT: A 1270 LYS cc_start: 0.7684 (mmmt) cc_final: 0.7394 (mttm) REVERT: A 1283 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7151 (m-10) REVERT: A 1473 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7928 (t-90) REVERT: A 1533 TRP cc_start: 0.8332 (OUTLIER) cc_final: 0.7865 (m-10) outliers start: 36 outliers final: 22 residues processed: 77 average time/residue: 0.1181 time to fit residues: 14.2013 Evaluate side-chains 71 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 648 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 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 1283 TYR Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1446 GLU Chi-restraints excluded: chain A residue 1473 HIS Chi-restraints excluded: chain A residue 1479 LYS 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 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.085129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.065399 restraints weight = 36798.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.067502 restraints weight = 20004.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068862 restraints weight = 13907.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.069702 restraints weight = 11097.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.070197 restraints weight = 9637.620| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2225 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= 0.124 Angle : 0.721 12.055 19484 Z= 0.330 Chirality : 0.062 0.611 2084 Planarity : 0.005 0.058 2315 Dihedral : 13.960 178.588 2434 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.86 % Allowed : 17.63 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.21), residues: 1526 helix: 1.43 (0.31), residues: 309 sheet: -1.37 (0.30), residues: 280 loop : -3.07 (0.17), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.010 0.001 TYR A 313 PHE 0.009 0.001 PHE A 747 TRP 0.009 0.001 TRP A1466 HIS 0.004 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14237) covalent geometry : angle 0.72137 / 0.33 (19484) hydrogen bonds : bond 0.03501 / 2.23 ( 342) hydrogen bonds : angle 3.90761 / 2.77 ( 905) *********************** 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 77 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.507 Fit side-chains REVERT: A 410 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7914 (pt) REVERT: A 989 ASP cc_start: 0.8106 (t70) cc_final: 0.7889 (t0) REVERT: A 1270 LYS cc_start: 0.7617 (mmmt) cc_final: 0.7333 (mttm) REVERT: A 1444 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9201 (m) REVERT: A 1473 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7873 (t-90) outliers start: 25 outliers final: 16 residues processed: 74 average time/residue: 0.1117 time to fit residues: 12.8772 Evaluate side-chains 63 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 44 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 410 LEU 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 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 1444 THR 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 1600 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 0.0040 chunk 50 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 131 optimal weight: 0.0020 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.081786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.061825 restraints weight = 36828.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063830 restraints weight = 20297.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.065105 restraints weight = 14308.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.065905 restraints weight = 11576.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.066313 restraints weight = 10151.820| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14237 Z= 0.221 Angle : 0.798 11.189 19484 Z= 0.372 Chirality : 0.071 0.720 2084 Planarity : 0.005 0.065 2315 Dihedral : 13.975 179.846 2434 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 2.31 % Allowed : 17.11 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.21), residues: 1526 helix: 1.35 (0.31), residues: 308 sheet: -1.56 (0.30), residues: 294 loop : -3.07 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.015 0.001 TYR A 863 PHE 0.020 0.002 PHE A1219 TRP 0.011 0.001 TRP A 977 HIS 0.006 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (14237) covalent geometry : angle 0.79833 / 0.37 (19484) hydrogen bonds : bond 0.04612 / 2.96 ( 342) hydrogen bonds : angle 4.15140 / 2.95 ( 905) *********************** 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 74 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 43 time to evaluate : 0.518 Fit side-chains REVERT: A 410 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7614 (pp) REVERT: A 989 ASP cc_start: 0.8142 (t70) cc_final: 0.7836 (t0) REVERT: A 1211 MET cc_start: 0.8165 (tmm) cc_final: 0.7333 (tmm) REVERT: A 1270 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7425 (mttm) REVERT: A 1473 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.7914 (t-90) outliers start: 31 outliers final: 24 residues processed: 71 average time/residue: 0.1050 time to fit residues: 11.8670 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR 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 410 LEU Chi-restraints excluded: chain A residue 504 ILE 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 1305 MET Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1446 GLU 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 1600 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 69 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064967 restraints weight = 36867.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.067099 restraints weight = 19749.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068460 restraints weight = 13629.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.069339 restraints weight = 10861.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069819 restraints weight = 9375.611| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2309 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 : 0.715 11.890 19484 Z= 0.328 Chirality : 0.062 0.635 2084 Planarity : 0.004 0.059 2315 Dihedral : 13.834 179.715 2434 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 1.79 % Allowed : 17.93 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.21), residues: 1526 helix: 1.56 (0.31), residues: 309 sheet: -1.24 (0.30), residues: 280 loop : -2.94 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 393 TYR 0.010 0.001 TYR A 313 PHE 0.012 0.001 PHE A1219 TRP 0.008 0.001 TRP A 42 HIS 0.005 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14237) covalent geometry : angle 0.71463 / 0.33 (19484) hydrogen bonds : bond 0.03543 / 2.25 ( 342) hydrogen bonds : angle 3.84482 / 2.72 ( 905) *********************** 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 68 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.523 Fit side-chains REVERT: A 410 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7871 (pt) REVERT: A 989 ASP cc_start: 0.8126 (t70) cc_final: 0.7811 (t0) REVERT: A 1211 MET cc_start: 0.8160 (tmm) cc_final: 0.7729 (tmm) REVERT: A 1270 LYS cc_start: 0.7600 (mmmt) cc_final: 0.7277 (mttm) REVERT: A 1473 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7907 (t-90) outliers start: 24 outliers final: 22 residues processed: 65 average time/residue: 0.1122 time to fit residues: 11.5143 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 648 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 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 1305 MET Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1446 GLU 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 1600 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 102 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.063387 restraints weight = 36754.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065419 restraints weight = 20142.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066743 restraints weight = 14142.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.067566 restraints weight = 11342.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.068101 restraints weight = 9905.953| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2212 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= 0.175 Angle : 0.748 11.632 19484 Z= 0.346 Chirality : 0.066 0.699 2084 Planarity : 0.005 0.063 2315 Dihedral : 13.831 179.200 2434 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 2.23 % Allowed : 17.56 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.21), residues: 1526 helix: 1.51 (0.31), residues: 309 sheet: -1.39 (0.30), residues: 292 loop : -2.91 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 393 TYR 0.012 0.001 TYR A 313 PHE 0.015 0.001 PHE A1219 TRP 0.010 0.001 TRP A 977 HIS 0.005 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (14237) covalent geometry : angle 0.74798 / 0.35 (19484) hydrogen bonds : bond 0.04103 / 2.63 ( 342) hydrogen bonds : angle 3.95518 / 2.81 ( 905) ********************** 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 72 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 42 time to evaluate : 0.530 Fit side-chains REVERT: A 410 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7452 (pp) REVERT: A 989 ASP cc_start: 0.8111 (t70) cc_final: 0.7808 (t0) REVERT: A 1211 MET cc_start: 0.8138 (tmm) cc_final: 0.7714 (tmm) REVERT: A 1270 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7384 (mttm) REVERT: A 1283 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.7186 (m-10) REVERT: A 1473 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7899 (t-90) REVERT: A 1533 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.7728 (m-10) outliers start: 30 outliers final: 23 residues processed: 69 average time/residue: 0.1079 time to fit residues: 11.9583 Evaluate side-chains 69 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 42 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 648 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 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 1367 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1446 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 125 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 0.0050 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063733 restraints weight = 36880.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065794 restraints weight = 20152.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.067121 restraints weight = 14076.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067952 restraints weight = 11293.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.068408 restraints weight = 9853.467| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2266 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= 0.162 Angle : 0.739 11.635 19484 Z= 0.341 Chirality : 0.065 0.679 2084 Planarity : 0.005 0.061 2315 Dihedral : 13.830 179.690 2434 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.23 % Allowed : 17.86 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.21), residues: 1526 helix: 1.39 (0.31), residues: 316 sheet: -1.16 (0.31), residues: 272 loop : -2.92 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.011 0.001 TYR A 313 PHE 0.015 0.001 PHE A1219 TRP 0.009 0.001 TRP A 42 HIS 0.005 0.001 HIS A1473 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (14237) covalent geometry : angle 0.73878 / 0.34 (19484) hydrogen bonds : bond 0.03975 / 2.55 ( 342) hydrogen bonds : angle 3.91738 / 2.78 ( 905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.55 seconds wall clock time: 36 minutes 44.61 seconds (2204.61 seconds total)