Starting phenix.real_space_refine on Sat Sep 12 10:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.cif" model { file = "/net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orn_13043/09_2026/7orn_13043.cif" } resolution = 2.8 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= 0.001 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 94 5.16 5 C 9262 2.51 5 N 2454 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.16s 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: 14811 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1700, 13900 Classifications: {'peptide': 1700} Link IDs: {'PTRANS': 60, 'TRANS': 1639} Chain breaks: 5 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 379 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 5, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 11} Conformer: "B" Number of residues, atoms: 18, 379 Classifications: {'RNAv2': 18} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 7, 'rna3p': 10} bond proxies already assigned to first conformer: 374 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 106 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3, 'water': 73} Link IDs: {None: 75} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A A T 18 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A T 18 " occ=0.50 residue: pdb=" P A C T 19 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B C T 19 " occ=0.50 Time building chain proxies: 2.83, per 1000 atoms: 0.19 Number of scatterers: 14811 At special positions: 0 Unit cell: (105.135, 105.135, 125.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 94 16.00 P 40 15.00 Mg 2 11.99 O 2959 8.00 N 2454 7.00 C 9262 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: 1.32 Conformation dependent library (CDL) restraints added in 524.4 milliseconds 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 14 sheets defined 57.4% alpha, 10.3% beta 8 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'A' and resid 18 through 46 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 99 through 121 removed outlier: 5.091A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 158 through 172 Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.570A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.742A pdb=" N MET A 214 " --> pdb=" O PHE A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 Processing helix chain 'A' and resid 237 through 260 removed outlier: 4.675A pdb=" N LYS A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ASP A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.595A pdb=" N ALA A 265 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 350 Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 475 through 489 removed outlier: 6.638A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 502 through 521 removed outlier: 3.698A pdb=" N GLN A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 620 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 626 through 639 removed outlier: 3.763A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.172A pdb=" N LEU A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 3.868A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 Processing helix chain 'A' and resid 680 through 698 removed outlier: 4.445A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 702 removed outlier: 3.866A pdb=" N GLN A 702 " --> pdb=" O ASP A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 702' Processing helix chain 'A' and resid 737 through 747 Processing helix chain 'A' and resid 748 through 751 Processing helix chain 'A' and resid 758 through 781 removed outlier: 4.309A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 811 Processing helix chain 'A' and resid 813 through 825 Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 849 through 854 Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.720A pdb=" N VAL A 879 " --> pdb=" O PRO A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 911 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.847A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 980 removed outlier: 3.900A pdb=" N GLU A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1020 removed outlier: 3.731A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A1002 " --> pdb=" O LEU A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1079 removed outlier: 3.952A pdb=" N TRP A1075 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1099 Processing helix chain 'A' and resid 1106 through 1114 Processing helix chain 'A' and resid 1123 through 1129 Processing helix chain 'A' and resid 1148 through 1174 Processing helix chain 'A' and resid 1201 through 1219 removed outlier: 3.512A pdb=" N ILE A1205 " --> pdb=" O GLU A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1262 Processing helix chain 'A' and resid 1267 through 1285 Processing helix chain 'A' and resid 1288 through 1307 Processing helix chain 'A' and resid 1325 through 1329 Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1340 through 1347 Processing helix chain 'A' and resid 1350 through 1365 Processing helix chain 'A' and resid 1366 through 1370 removed outlier: 3.563A pdb=" N LYS A1370 " --> pdb=" O VAL A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1380 removed outlier: 3.770A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1385 through 1389 Processing helix chain 'A' and resid 1390 through 1404 removed outlier: 3.512A pdb=" N VAL A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1440 removed outlier: 3.627A pdb=" N LYS A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1452 Processing helix chain 'A' and resid 1455 through 1467 Processing helix chain 'A' and resid 1468 through 1473 removed outlier: 4.118A pdb=" N VAL A1472 " --> pdb=" O PRO A1468 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1491 through 1498 Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.589A pdb=" N ILE A1511 " --> pdb=" O PHE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1563 removed outlier: 3.612A pdb=" N LEU A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1578 Processing helix chain 'A' and resid 1581 through 1593 Processing helix chain 'A' and resid 1612 through 1617 Processing helix chain 'A' and resid 1622 through 1633 Processing helix chain 'A' and resid 1641 through 1659 removed outlier: 3.507A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1677 Processing helix chain 'A' and resid 1680 through 1703 removed outlier: 3.567A pdb=" N GLU A1703 " --> pdb=" O VAL A1699 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1729 removed outlier: 3.513A pdb=" N LEU A1729 " --> pdb=" O MET A1725 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.332A pdb=" N LEU A 88 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 127 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE A 90 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE A 129 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP A 92 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE A 131 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYS A 94 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 388 removed outlier: 4.882A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 561 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 removed outlier: 4.882A pdb=" N LEU A 392 " --> pdb=" O MET A 400 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AA6, first strand: chain 'A' and resid 710 through 711 removed outlier: 6.648A pdb=" N TYR A 710 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 728 Processing sheet with id=AA8, first strand: chain 'A' and resid 842 through 846 Processing sheet with id=AA9, first strand: chain 'A' and resid 871 through 872 Processing sheet with id=AB1, first strand: chain 'A' and resid 959 through 962 removed outlier: 6.443A pdb=" N PHE A 945 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1235 through 1238 Processing sheet with id=AB3, first strand: chain 'A' and resid 1594 through 1601 removed outlier: 4.906A pdb=" N THR A1737 " --> pdb=" O GLY A1597 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP A1735 " --> pdb=" O PRO A1599 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1606 through 1608 Processing sheet with id=AB5, first strand: chain 'A' and resid 2087 through 2090 removed outlier: 4.316A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2579 1.33 - 1.45: 3959 1.45 - 1.57: 8324 1.57 - 1.69: 78 1.69 - 1.81: 157 Bond restraints: 15097 Sorted by residual: bond pdb=" N THR A2093 " pdb=" CA THR A2093 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.06e+01 bond pdb=" N ILE A2095 " pdb=" CA ILE A2095 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.92e+00 bond pdb=" N ARG A1141 " pdb=" CA ARG A1141 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.26e-02 6.30e+03 9.26e+00 bond pdb=" N ILE A1378 " pdb=" CA ILE A1378 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 8.30e+00 bond pdb=" N ILE A 518 " pdb=" CA ILE A 518 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.88e+00 ... (remaining 15092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 20242 2.49 - 4.98: 295 4.98 - 7.48: 9 7.48 - 9.97: 1 9.97 - 12.46: 1 Bond angle restraints: 20548 Sorted by residual: angle pdb=" N PRO A2094 " pdb=" CA PRO A2094 " pdb=" C PRO A2094 " ideal model delta sigma weight residual 112.47 100.01 12.46 2.06e+00 2.36e-01 3.66e+01 angle pdb=" CA ILE A1578 " pdb=" C ILE A1578 " pdb=" O ILE A1578 " ideal model delta sigma weight residual 120.70 117.39 3.31 8.50e-01 1.38e+00 1.51e+01 angle pdb=" C THR A1365 " pdb=" CA THR A1365 " pdb=" CB THR A1365 " ideal model delta sigma weight residual 109.41 115.59 -6.18 1.62e+00 3.81e-01 1.46e+01 angle pdb=" N GLY A 720 " pdb=" CA GLY A 720 " pdb=" C GLY A 720 " ideal model delta sigma weight residual 111.56 115.40 -3.84 1.01e+00 9.80e-01 1.44e+01 angle pdb=" C3' A T 20 " pdb=" O3' A T 20 " pdb=" P C T 21 " ideal model delta sigma weight residual 119.70 124.24 -4.54 1.20e+00 6.94e-01 1.43e+01 ... (remaining 20543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8305 17.69 - 35.39: 630 35.39 - 53.08: 122 53.08 - 70.77: 57 70.77 - 88.46: 16 Dihedral angle restraints: 9130 sinusoidal: 4069 harmonic: 5061 Sorted by residual: dihedral pdb=" C4' C T 21 " pdb=" C3' C T 21 " pdb=" C2' C T 21 " pdb=" C1' C T 21 " ideal model delta sinusoidal sigma weight residual 36.34 -41.57 77.92 1 3.10e+00 1.04e-01 7.90e+02 dihedral pdb=" C4' U T 22 " pdb=" C3' U T 22 " pdb=" C2' U T 22 " pdb=" C1' U T 22 " ideal model delta sinusoidal sigma weight residual 36.34 -37.83 74.18 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4'B C T 19 " pdb=" C3'B C T 19 " pdb=" C2'B C T 19 " pdb=" C1'B C T 19 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.69 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 9127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2003 0.066 - 0.132: 219 0.132 - 0.197: 27 0.197 - 0.263: 50 0.263 - 0.329: 13 Chirality restraints: 2312 Sorted by residual: chirality pdb=" CA THR A 552 " pdb=" N THR A 552 " pdb=" C THR A 552 " pdb=" CB THR A 552 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C2' U T 22 " pdb=" C3' U T 22 " pdb=" O2' U T 22 " pdb=" C1' U T 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA LEU A1144 " pdb=" N LEU A1144 " pdb=" C LEU A1144 " pdb=" CB LEU A1144 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2309 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1143 " -0.024 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP A1143 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1143 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A1143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1143 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A1143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1143 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1143 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A1143 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1140 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C LYS A1140 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A1140 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A1141 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1187 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASP A1187 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A1187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A1188 " -0.011 2.00e-02 2.50e+03 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 80 2.56 - 3.15: 11576 3.15 - 3.73: 23923 3.73 - 4.32: 35684 4.32 - 4.90: 57179 Nonbonded interactions: 128442 Sorted by model distance: nonbonded pdb=" O1B ATP A2301 " pdb="MG MG A2303 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP A1060 " pdb="MG MG A2303 " model vdw 2.089 2.170 nonbonded pdb=" OD1 ASP A1187 " pdb="MG MG A2302 " model vdw 2.115 2.170 nonbonded pdb=" OD2 ASP A1187 " pdb="MG MG A2303 " model vdw 2.157 2.170 nonbonded pdb=" OD1 ASP A1060 " pdb="MG MG A2302 " model vdw 2.191 2.170 ... (remaining 128437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.900 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 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 : 0.004 0.044 15097 Z= 0.220 Angle : 0.647 12.461 20548 Z= 0.383 Chirality : 0.058 0.329 2312 Planarity : 0.004 0.042 2461 Dihedral : 14.030 88.463 5844 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.19 % Allowed : 0.32 % Favored : 99.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1688 helix: 1.71 (0.18), residues: 891 sheet: 1.21 (0.43), residues: 140 loop : -0.66 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.018 0.001 TYR A1442 PHE 0.019 0.001 PHE A1395 TRP 0.035 0.001 TRP A1143 HIS 0.004 0.001 HIS A 814 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.22 (15097) covalent geometry : angle 0.64715 / 0.38 (20548) hydrogen bonds : bond 0.14135 / 9.61 ( 763) hydrogen bonds : angle 5.34372 / 3.77 ( 2206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.533 Fit side-chains REVERT: A 35 ASP cc_start: 0.6259 (m-30) cc_final: 0.6033 (m-30) REVERT: A 487 ASP cc_start: 0.7454 (m-30) cc_final: 0.7103 (m-30) REVERT: A 1160 MET cc_start: 0.8822 (mmp) cc_final: 0.8477 (mmp) REVERT: A 1258 THR cc_start: 0.8674 (m) cc_final: 0.8406 (m) outliers start: 3 outliers final: 0 residues processed: 233 average time/residue: 0.7172 time to fit residues: 181.4060 Evaluate side-chains 184 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 ASN A 289 GLN A 424 HIS A 497 HIS A1620 HIS A1658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.117500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.092135 restraints weight = 19528.037| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.34 r_work: 0.2709 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15097 Z= 0.161 Angle : 0.752 21.937 20548 Z= 0.342 Chirality : 0.073 1.370 2312 Planarity : 0.004 0.038 2461 Dihedral : 10.324 139.121 2294 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.95 % Allowed : 7.89 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1688 helix: 2.01 (0.17), residues: 898 sheet: 1.38 (0.44), residues: 129 loop : -0.65 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1017 TYR 0.018 0.001 TYR A1576 PHE 0.019 0.001 PHE A1395 TRP 0.025 0.001 TRP A1143 HIS 0.010 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (15097) covalent geometry : angle 0.75220 / 0.34 (20548) hydrogen bonds : bond 0.04870 / 3.26 ( 763) hydrogen bonds : angle 4.13919 / 2.93 ( 2206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.518 Fit side-chains REVERT: A 23 LYS cc_start: 0.7850 (tmmt) cc_final: 0.7545 (ttpp) REVERT: A 35 ASP cc_start: 0.6617 (m-30) cc_final: 0.6250 (m-30) REVERT: A 329 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8239 (mmtp) REVERT: A 487 ASP cc_start: 0.8466 (m-30) cc_final: 0.8134 (m-30) REVERT: A 597 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7816 (p0) REVERT: A 1017 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.6883 (mtm180) REVERT: A 1188 ASP cc_start: 0.8444 (m-30) cc_final: 0.8212 (m-30) REVERT: A 1258 THR cc_start: 0.8973 (m) cc_final: 0.8651 (m) REVERT: A 1262 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7172 (m-30) REVERT: A 1665 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9108 (ttt) outliers start: 15 outliers final: 4 residues processed: 202 average time/residue: 0.6909 time to fit residues: 151.6650 Evaluate side-chains 186 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 179 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 164 optimal weight: 0.0870 chunk 7 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 46 ASN A 159 ASN A1448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.115862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.090382 restraints weight = 18398.693| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.30 r_work: 0.2709 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 15097 Z= 0.171 Angle : 0.677 16.573 20548 Z= 0.320 Chirality : 0.057 0.715 2312 Planarity : 0.004 0.037 2461 Dihedral : 10.746 162.766 2294 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.40 % Allowed : 9.35 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1688 helix: 2.03 (0.17), residues: 898 sheet: 1.37 (0.44), residues: 126 loop : -0.73 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.019 0.001 TYR A1576 PHE 0.019 0.001 PHE A1395 TRP 0.020 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (15097) covalent geometry : angle 0.67670 / 0.32 (20548) hydrogen bonds : bond 0.04787 / 3.19 ( 763) hydrogen bonds : angle 4.06143 / 2.88 ( 2206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.510 Fit side-chains REVERT: A 23 LYS cc_start: 0.7892 (tmmt) cc_final: 0.7662 (ttpp) REVERT: A 35 ASP cc_start: 0.6585 (m-30) cc_final: 0.6264 (m-30) REVERT: A 329 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8229 (mmtp) REVERT: A 487 ASP cc_start: 0.8490 (m-30) cc_final: 0.8197 (m-30) REVERT: A 597 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 1258 THR cc_start: 0.8993 (m) cc_final: 0.8668 (m) REVERT: A 1262 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: A 1665 MET cc_start: 0.9350 (ttm) cc_final: 0.9109 (ttt) REVERT: A 1734 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8124 (pp20) outliers start: 22 outliers final: 5 residues processed: 202 average time/residue: 0.6739 time to fit residues: 148.4824 Evaluate side-chains 191 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 183 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 46 ASN A 159 ASN A 506 GLN A 523 GLN A1007 GLN A1502 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.115080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.087957 restraints weight = 28109.865| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.76 r_work: 0.2652 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15097 Z= 0.181 Angle : 0.657 16.811 20548 Z= 0.316 Chirality : 0.055 0.616 2312 Planarity : 0.004 0.041 2461 Dihedral : 11.015 158.301 2294 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.40 % Allowed : 10.75 % Favored : 87.85 % 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: 1.37 (0.20), residues: 1688 helix: 2.03 (0.17), residues: 897 sheet: 1.27 (0.44), residues: 120 loop : -0.72 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1017 TYR 0.021 0.002 TYR A1576 PHE 0.019 0.002 PHE A1395 TRP 0.021 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (15097) covalent geometry : angle 0.65675 / 0.32 (20548) hydrogen bonds : bond 0.04794 / 3.19 ( 763) hydrogen bonds : angle 4.05941 / 2.88 ( 2206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.555 Fit side-chains REVERT: A 23 LYS cc_start: 0.7918 (tmmt) cc_final: 0.7661 (ttpp) REVERT: A 35 ASP cc_start: 0.6685 (m-30) cc_final: 0.6360 (m-30) REVERT: A 329 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8217 (mmtp) REVERT: A 359 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 487 ASP cc_start: 0.8566 (m-30) cc_final: 0.8287 (m-30) REVERT: A 597 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7964 (p0) REVERT: A 779 GLU cc_start: 0.8134 (pt0) cc_final: 0.7771 (mp0) REVERT: A 1017 ARG cc_start: 0.7450 (mtp-110) cc_final: 0.6851 (mtm180) REVERT: A 1056 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: A 1258 THR cc_start: 0.9019 (m) cc_final: 0.8686 (m) REVERT: A 1262 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7070 (m-30) REVERT: A 1601 ARG cc_start: 0.8350 (ptm160) cc_final: 0.8069 (ppp80) REVERT: A 1665 MET cc_start: 0.9365 (ttm) cc_final: 0.9124 (ttt) REVERT: A 1734 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8323 (pp20) outliers start: 22 outliers final: 6 residues processed: 203 average time/residue: 0.6721 time to fit residues: 148.7264 Evaluate side-chains 196 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 171 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 46 ASN A 159 ASN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.114591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.087670 restraints weight = 26426.806| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.69 r_work: 0.2656 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 15097 Z= 0.185 Angle : 0.650 17.435 20548 Z= 0.314 Chirality : 0.054 0.555 2312 Planarity : 0.004 0.043 2461 Dihedral : 11.199 162.551 2294 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.53 % Allowed : 11.39 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1688 helix: 2.02 (0.17), residues: 897 sheet: 1.22 (0.44), residues: 120 loop : -0.75 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.021 0.002 TYR A1576 PHE 0.019 0.002 PHE A1395 TRP 0.021 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (15097) covalent geometry : angle 0.65041 / 0.31 (20548) hydrogen bonds : bond 0.04806 / 3.19 ( 763) hydrogen bonds : angle 4.06515 / 2.88 ( 2206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.435 Fit side-chains REVERT: A 23 LYS cc_start: 0.7957 (tmmt) cc_final: 0.7670 (ttpp) REVERT: A 35 ASP cc_start: 0.6749 (m-30) cc_final: 0.6410 (m-30) REVERT: A 46 ASN cc_start: 0.8290 (m-40) cc_final: 0.7915 (t0) REVERT: A 125 GLU cc_start: 0.8246 (tp30) cc_final: 0.7960 (tp30) REVERT: A 329 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8232 (mmtp) REVERT: A 359 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: A 487 ASP cc_start: 0.8586 (m-30) cc_final: 0.8323 (m-30) REVERT: A 597 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7977 (p0) REVERT: A 779 GLU cc_start: 0.8096 (pt0) cc_final: 0.7826 (mp0) REVERT: A 1056 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: A 1258 THR cc_start: 0.9019 (m) cc_final: 0.8681 (m) REVERT: A 1262 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7069 (m-30) REVERT: A 1601 ARG cc_start: 0.8366 (ptm160) cc_final: 0.8075 (ppp80) REVERT: A 1634 ASN cc_start: 0.8622 (t0) cc_final: 0.8371 (t0) REVERT: A 1734 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8387 (pp20) outliers start: 24 outliers final: 10 residues processed: 209 average time/residue: 0.6607 time to fit residues: 150.0520 Evaluate side-chains 200 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 159 ASN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.117846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092577 restraints weight = 17937.058| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.26 r_work: 0.2752 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15097 Z= 0.117 Angle : 0.581 14.958 20548 Z= 0.281 Chirality : 0.049 0.474 2312 Planarity : 0.003 0.038 2461 Dihedral : 11.324 172.109 2294 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.59 % Allowed : 11.70 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1688 helix: 2.20 (0.17), residues: 900 sheet: 1.35 (0.45), residues: 120 loop : -0.64 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1017 TYR 0.015 0.001 TYR A1576 PHE 0.017 0.001 PHE A1395 TRP 0.021 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15097) covalent geometry : angle 0.58114 / 0.28 (20548) hydrogen bonds : bond 0.03891 / 2.57 ( 763) hydrogen bonds : angle 3.86382 / 2.74 ( 2206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.555 Fit side-chains REVERT: A 35 ASP cc_start: 0.6573 (m-30) cc_final: 0.6272 (m-30) REVERT: A 46 ASN cc_start: 0.8244 (m-40) cc_final: 0.7896 (t0) REVERT: A 125 GLU cc_start: 0.8164 (tp30) cc_final: 0.7870 (tp30) REVERT: A 329 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8174 (mmtp) REVERT: A 359 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 487 ASP cc_start: 0.8462 (m-30) cc_final: 0.8200 (m-30) REVERT: A 597 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7798 (p0) REVERT: A 995 ASP cc_start: 0.7837 (m-30) cc_final: 0.7558 (m-30) REVERT: A 1017 ARG cc_start: 0.7370 (mtp-110) cc_final: 0.6892 (mtm180) REVERT: A 1056 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: A 1258 THR cc_start: 0.8964 (m) cc_final: 0.8643 (m) REVERT: A 1262 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6929 (m-30) REVERT: A 1365 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 1601 ARG cc_start: 0.8317 (ptm160) cc_final: 0.8026 (ppp80) REVERT: A 1606 SER cc_start: 0.9270 (m) cc_final: 0.9052 (t) REVERT: A 1634 ASN cc_start: 0.8601 (t0) cc_final: 0.8361 (t0) REVERT: A 1725 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7663 (tmm) outliers start: 25 outliers final: 6 residues processed: 210 average time/residue: 0.6339 time to fit residues: 145.5273 Evaluate side-chains 193 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 148 optimal weight: 0.0050 chunk 146 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 159 ASN A 506 GLN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.120258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095003 restraints weight = 16788.327| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.30 r_work: 0.2777 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2683 r_free = 0.2683 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15097 Z= 0.115 Angle : 0.572 14.506 20548 Z= 0.276 Chirality : 0.048 0.492 2312 Planarity : 0.003 0.041 2461 Dihedral : 11.294 177.105 2294 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.84 % Allowed : 11.90 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.21), residues: 1688 helix: 2.26 (0.17), residues: 900 sheet: 1.56 (0.46), residues: 117 loop : -0.59 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.017 0.001 TYR A1576 PHE 0.017 0.001 PHE A1395 TRP 0.018 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15097) covalent geometry : angle 0.57170 / 0.28 (20548) hydrogen bonds : bond 0.03794 / 2.51 ( 763) hydrogen bonds : angle 3.79885 / 2.69 ( 2206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.546 Fit side-chains REVERT: A 35 ASP cc_start: 0.6535 (m-30) cc_final: 0.6232 (m-30) REVERT: A 46 ASN cc_start: 0.8253 (m-40) cc_final: 0.7923 (t0) REVERT: A 125 GLU cc_start: 0.8150 (tp30) cc_final: 0.7881 (tp30) REVERT: A 329 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8317 (mmtp) REVERT: A 359 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: A 487 ASP cc_start: 0.8467 (m-30) cc_final: 0.8195 (m-30) REVERT: A 597 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7750 (p0) REVERT: A 995 ASP cc_start: 0.7716 (m-30) cc_final: 0.7385 (m-30) REVERT: A 1017 ARG cc_start: 0.7438 (mtp-110) cc_final: 0.6950 (mtm180) REVERT: A 1056 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: A 1080 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 1258 THR cc_start: 0.8995 (m) cc_final: 0.8771 (m) REVERT: A 1365 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8381 (m) REVERT: A 1601 ARG cc_start: 0.8359 (ptm160) cc_final: 0.8085 (ppp80) REVERT: A 1606 SER cc_start: 0.9279 (m) cc_final: 0.9079 (t) REVERT: A 1612 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 1634 ASN cc_start: 0.8606 (t0) cc_final: 0.8398 (t0) REVERT: A 1665 MET cc_start: 0.9342 (ttm) cc_final: 0.9085 (ttt) REVERT: A 1725 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7619 (tmm) REVERT: A 1734 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8349 (pp20) outliers start: 29 outliers final: 8 residues processed: 212 average time/residue: 0.6762 time to fit residues: 156.7441 Evaluate side-chains 196 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 42 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 159 ASN A1007 GLN A1620 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.091710 restraints weight = 18992.579| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 1.40 r_work: 0.2698 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 15097 Z= 0.166 Angle : 0.624 16.404 20548 Z= 0.302 Chirality : 0.052 0.520 2312 Planarity : 0.004 0.040 2461 Dihedral : 11.349 176.646 2294 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.40 % Allowed : 12.34 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.20), residues: 1688 helix: 2.15 (0.17), residues: 898 sheet: 1.48 (0.45), residues: 123 loop : -0.68 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 136 TYR 0.019 0.001 TYR A1576 PHE 0.019 0.001 PHE A1395 TRP 0.016 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (15097) covalent geometry : angle 0.62369 / 0.30 (20548) hydrogen bonds : bond 0.04508 / 3.00 ( 763) hydrogen bonds : angle 3.95694 / 2.80 ( 2206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.486 Fit side-chains REVERT: A 35 ASP cc_start: 0.6785 (m-30) cc_final: 0.6508 (m-30) REVERT: A 46 ASN cc_start: 0.8303 (m-40) cc_final: 0.7983 (t0) REVERT: A 125 GLU cc_start: 0.8330 (tp30) cc_final: 0.8070 (tp30) REVERT: A 359 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 487 ASP cc_start: 0.8661 (m-30) cc_final: 0.8419 (m-30) REVERT: A 597 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7968 (p0) REVERT: A 1017 ARG cc_start: 0.7559 (mtp-110) cc_final: 0.7085 (mtm180) REVERT: A 1056 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: A 1080 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8545 (t0) REVERT: A 1258 THR cc_start: 0.9024 (m) cc_final: 0.8791 (m) REVERT: A 1601 ARG cc_start: 0.8432 (ptm160) cc_final: 0.8153 (ppp80) REVERT: A 1665 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9117 (ttt) REVERT: A 1725 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7836 (tmm) REVERT: A 1734 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (pp20) outliers start: 22 outliers final: 10 residues processed: 192 average time/residue: 0.6571 time to fit residues: 138.5215 Evaluate side-chains 193 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1725 MET Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 44 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 159 ASN A1007 GLN A1620 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.118863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.093581 restraints weight = 18919.211| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.31 r_work: 0.2723 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15097 Z= 0.131 Angle : 0.590 15.445 20548 Z= 0.285 Chirality : 0.049 0.489 2312 Planarity : 0.003 0.038 2461 Dihedral : 11.405 176.984 2294 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.34 % Allowed : 12.53 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.21), residues: 1688 helix: 2.22 (0.17), residues: 899 sheet: 1.45 (0.45), residues: 126 loop : -0.67 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.016 0.001 TYR A1576 PHE 0.018 0.001 PHE A1395 TRP 0.019 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (15097) covalent geometry : angle 0.58968 / 0.29 (20548) hydrogen bonds : bond 0.04028 / 2.67 ( 763) hydrogen bonds : angle 3.86660 / 2.74 ( 2206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.539 Fit side-chains REVERT: A 35 ASP cc_start: 0.6748 (m-30) cc_final: 0.6470 (m-30) REVERT: A 46 ASN cc_start: 0.8264 (m-40) cc_final: 0.7956 (t0) REVERT: A 125 GLU cc_start: 0.8282 (tp30) cc_final: 0.8014 (tp30) REVERT: A 359 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: A 487 ASP cc_start: 0.8595 (m-30) cc_final: 0.8352 (m-30) REVERT: A 597 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7939 (p0) REVERT: A 1017 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7081 (mtm180) REVERT: A 1056 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: A 1080 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 1258 THR cc_start: 0.8999 (m) cc_final: 0.8693 (m) REVERT: A 1262 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7068 (m-30) REVERT: A 1365 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8450 (m) REVERT: A 1601 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8151 (ppp80) REVERT: A 1665 MET cc_start: 0.9348 (ttm) cc_final: 0.9128 (ttt) REVERT: A 1725 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7854 (tmm) REVERT: A 1734 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8480 (pp20) outliers start: 21 outliers final: 9 residues processed: 191 average time/residue: 0.6340 time to fit residues: 132.9941 Evaluate side-chains 193 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 73 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 108 optimal weight: 0.0770 chunk 93 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 159 ASN A1007 GLN A1620 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.093555 restraints weight = 23662.371| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.53 r_work: 0.2691 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15097 Z= 0.123 Angle : 0.579 15.044 20548 Z= 0.280 Chirality : 0.049 0.484 2312 Planarity : 0.003 0.038 2461 Dihedral : 11.382 177.002 2294 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.08 % Allowed : 13.17 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.21), residues: 1688 helix: 2.26 (0.17), residues: 899 sheet: 1.49 (0.45), residues: 126 loop : -0.64 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.015 0.001 TYR A1576 PHE 0.017 0.001 PHE A1395 TRP 0.019 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15097) covalent geometry : angle 0.57898 / 0.28 (20548) hydrogen bonds : bond 0.03895 / 2.58 ( 763) hydrogen bonds : angle 3.82768 / 2.71 ( 2206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3376 Ramachandran restraints generated. 1688 Oldfield, 0 Emsley, 1688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.701 Fit side-chains REVERT: A 35 ASP cc_start: 0.6849 (m-30) cc_final: 0.6586 (m-30) REVERT: A 46 ASN cc_start: 0.8297 (m-40) cc_final: 0.7972 (t0) REVERT: A 125 GLU cc_start: 0.8356 (tp30) cc_final: 0.8124 (tp30) REVERT: A 359 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 487 ASP cc_start: 0.8688 (m-30) cc_final: 0.8461 (m-30) REVERT: A 597 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 1017 ARG cc_start: 0.7541 (mtp-110) cc_final: 0.7092 (mtm180) REVERT: A 1056 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: A 1080 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 1258 THR cc_start: 0.9017 (m) cc_final: 0.8724 (m) REVERT: A 1262 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: A 1365 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8439 (m) REVERT: A 1601 ARG cc_start: 0.8489 (ptm160) cc_final: 0.8218 (ppp80) REVERT: A 1665 MET cc_start: 0.9362 (ttm) cc_final: 0.9148 (ttt) REVERT: A 1725 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7954 (tmm) REVERT: A 1734 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8530 (pp20) outliers start: 17 outliers final: 8 residues processed: 190 average time/residue: 0.6133 time to fit residues: 127.9540 Evaluate side-chains 193 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 146 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.118784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094084 restraints weight = 19605.686| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.29 r_work: 0.2712 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15097 Z= 0.133 Angle : 0.587 15.388 20548 Z= 0.284 Chirality : 0.049 0.487 2312 Planarity : 0.003 0.037 2461 Dihedral : 11.383 176.998 2294 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.21 % Allowed : 13.30 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.21), residues: 1688 helix: 2.24 (0.17), residues: 899 sheet: 1.49 (0.45), residues: 126 loop : -0.65 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.016 0.001 TYR A1576 PHE 0.018 0.001 PHE A1395 TRP 0.018 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (15097) covalent geometry : angle 0.58670 / 0.28 (20548) hydrogen bonds : bond 0.04040 / 2.68 ( 763) hydrogen bonds : angle 3.84823 / 2.72 ( 2206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5866.06 seconds wall clock time: 100 minutes 45.56 seconds (6045.56 seconds total)