Starting phenix.real_space_refine on Fri Jul 3 17:32:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7orn_13043/07_2026/7orn_13043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orn_13043/07_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_13043/07_2026/7orn_13043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orn_13043/07_2026/7orn_13043.map" model { file = "/net/cci-nas-00/data/ceres_data/7orn_13043/07_2026/7orn_13043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orn_13043/07_2026/7orn_13043.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7orn_13043/07_2026/7orn_13043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7orn_13043/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: 2.25, per 1000 atoms: 0.15 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: 0.87 Conformation dependent library (CDL) restraints added in 435.3 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: 1.72 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: 2.49 Time building geometry restraints manager: 1.18 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: 20342 2.49 - 4.98: 199 4.98 - 7.48: 6 7.48 - 9.97: 0 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=" C2' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " ideal model delta sigma weight residual 114.00 121.42 -7.42 1.50e+00 4.44e-01 2.45e+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 ... (remaining 20543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8395 17.69 - 35.39: 610 35.39 - 53.08: 92 53.08 - 70.77: 27 70.77 - 88.46: 6 Dihedral angle restraints: 9130 sinusoidal: 4069 harmonic: 5061 Sorted by residual: dihedral pdb=" O4' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " pdb=" C2 C T 21 " ideal model delta sinusoidal sigma weight residual 232.00 152.16 79.84 1 1.70e+01 3.46e-03 2.74e+01 dihedral pdb=" C THR A 552 " pdb=" N THR A 552 " pdb=" CA THR A 552 " pdb=" CB THR A 552 " ideal model delta harmonic sigma weight residual -122.00 -132.94 10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" C LEU A1144 " pdb=" N LEU A1144 " pdb=" CA LEU A1144 " pdb=" CB LEU A1144 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 9127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2062 0.066 - 0.132: 218 0.132 - 0.197: 25 0.197 - 0.263: 4 0.263 - 0.329: 3 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=" 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 chirality pdb=" CA TRP A1143 " pdb=" N TRP A1143 " pdb=" C TRP A1143 " pdb=" CB TRP A1143 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+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: 4.970 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.530 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- 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= 0.218 Angle : 0.592 12.461 20548 Z= 0.372 Chirality : 0.044 0.329 2312 Planarity : 0.004 0.042 2461 Dihedral : 12.578 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 0.00366 / 0.22 (15097) covalent geometry : angle 0.59177 / 0.37 (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 : 0.351 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: 0.6189 time to fit residues: 156.6353 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 : 0.419 ------------------------------------------------------------------------------- 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: 2.9990 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 = 0.3238 r_free = 0.3238 target = 0.116088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.089970 restraints weight = 19110.433| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.39 r_work: 0.2723 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15097 Z= 0.144 Angle : 0.507 8.346 20548 Z= 0.273 Chirality : 0.041 0.228 2312 Planarity : 0.004 0.038 2461 Dihedral : 7.118 86.235 2294 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.08 % Allowed : 7.82 % Favored : 91.09 % 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: 1.42 (0.21), residues: 1688 helix: 2.00 (0.17), residues: 898 sheet: 1.37 (0.44), residues: 129 loop : -0.65 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1017 TYR 0.018 0.001 TYR A1576 PHE 0.019 0.001 PHE A1395 TRP 0.023 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (15097) covalent geometry : angle 0.50731 / 0.27 (20548) hydrogen bonds : bond 0.04689 / 3.13 ( 763) hydrogen bonds : angle 4.11172 / 2.91 ( 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: 17 poor density : 192 time to evaluate : 0.570 Fit side-chains REVERT: A 23 LYS cc_start: 0.7833 (tmmt) cc_final: 0.7526 (ttpp) REVERT: A 35 ASP cc_start: 0.6584 (m-30) cc_final: 0.6216 (m-30) REVERT: A 329 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8245 (mmtp) REVERT: A 487 ASP cc_start: 0.8453 (m-30) cc_final: 0.8144 (m-30) REVERT: A 597 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7767 (p0) REVERT: A 1258 THR cc_start: 0.8964 (m) cc_final: 0.8642 (m) REVERT: A 1262 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: A 1469 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: A 1665 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9131 (ttt) outliers start: 17 outliers final: 5 residues processed: 203 average time/residue: 0.6460 time to fit residues: 142.7045 Evaluate side-chains 190 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 997 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1469 GLU 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: 3.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 164 optimal weight: 0.0010 chunk 7 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 46 ASN A 159 ASN A 506 GLN A1448 GLN A1620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.088963 restraints weight = 17780.540| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.28 r_work: 0.2673 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15097 Z= 0.180 Angle : 0.526 8.288 20548 Z= 0.283 Chirality : 0.042 0.243 2312 Planarity : 0.004 0.041 2461 Dihedral : 7.334 87.991 2294 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.46 % Allowed : 9.41 % Favored : 89.12 % 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: 1.33 (0.20), residues: 1688 helix: 1.99 (0.17), residues: 898 sheet: 1.29 (0.45), residues: 120 loop : -0.74 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.020 0.002 TYR A1576 PHE 0.020 0.002 PHE A1395 TRP 0.020 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (15097) covalent geometry : angle 0.52641 / 0.28 (20548) hydrogen bonds : bond 0.04992 / 3.34 ( 763) hydrogen bonds : angle 4.10937 / 2.91 ( 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 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.591 Fit side-chains REVERT: A 23 LYS cc_start: 0.7913 (tmmt) cc_final: 0.7686 (ttpp) REVERT: A 35 ASP cc_start: 0.6618 (m-30) cc_final: 0.6290 (m-30) REVERT: A 329 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8261 (mmtp) REVERT: A 487 ASP cc_start: 0.8526 (m-30) cc_final: 0.8236 (m-30) REVERT: A 597 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 1258 THR cc_start: 0.9006 (m) cc_final: 0.8680 (m) REVERT: A 1262 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: A 1469 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: A 1665 MET cc_start: 0.9354 (ttm) cc_final: 0.9107 (ttt) REVERT: A 1734 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8238 (pp20) outliers start: 23 outliers final: 6 residues processed: 203 average time/residue: 0.5900 time to fit residues: 130.6956 Evaluate side-chains 193 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 988 GLU 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 1469 GLU 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: 2.9990 chunk 91 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.114708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.088605 restraints weight = 21541.257| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.45 r_work: 0.2698 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15097 Z= 0.149 Angle : 0.494 8.385 20548 Z= 0.266 Chirality : 0.041 0.256 2312 Planarity : 0.004 0.037 2461 Dihedral : 7.316 88.284 2294 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.21 % Allowed : 11.01 % Favored : 87.79 % 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: 1.41 (0.20), residues: 1688 helix: 2.06 (0.17), residues: 898 sheet: 1.30 (0.45), residues: 120 loop : -0.72 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1017 TYR 0.019 0.001 TYR A1576 PHE 0.019 0.001 PHE A1395 TRP 0.020 0.001 TRP A1143 HIS 0.010 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (15097) covalent geometry : angle 0.49434 / 0.27 (20548) hydrogen bonds : bond 0.04481 / 2.98 ( 763) hydrogen bonds : angle 3.99847 / 2.83 ( 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 207 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.538 Fit side-chains REVERT: A 35 ASP cc_start: 0.6589 (m-30) cc_final: 0.6273 (m-30) REVERT: A 46 ASN cc_start: 0.8291 (m-40) cc_final: 0.7895 (t0) REVERT: A 125 GLU cc_start: 0.8151 (tp30) cc_final: 0.7861 (tp30) REVERT: A 329 LYS cc_start: 0.8517 (mtmt) cc_final: 0.8221 (mmtp) REVERT: A 359 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: A 487 ASP cc_start: 0.8494 (m-30) cc_final: 0.8194 (m-30) REVERT: A 566 LYS cc_start: 0.8703 (tptp) cc_final: 0.8449 (tptp) REVERT: A 597 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7821 (p0) REVERT: A 779 GLU cc_start: 0.8066 (pt0) cc_final: 0.7735 (mp0) REVERT: A 1017 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.6844 (mtm180) REVERT: A 1056 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: A 1258 THR cc_start: 0.8981 (m) cc_final: 0.8647 (m) REVERT: A 1262 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: A 1469 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: A 1601 ARG cc_start: 0.8326 (ptp-110) cc_final: 0.8031 (ppp80) REVERT: A 1665 MET cc_start: 0.9356 (ttm) cc_final: 0.9101 (ttt) REVERT: A 1734 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8361 (pp20) outliers start: 19 outliers final: 5 residues processed: 201 average time/residue: 0.6170 time to fit residues: 135.4336 Evaluate side-chains 199 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 1469 GLU 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: 6.9990 chunk 87 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.114027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.088441 restraints weight = 18461.895| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.31 r_work: 0.2676 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15097 Z= 0.173 Angle : 0.513 8.418 20548 Z= 0.276 Chirality : 0.041 0.261 2312 Planarity : 0.004 0.042 2461 Dihedral : 7.478 88.844 2294 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.46 % Allowed : 11.39 % Favored : 87.15 % 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: 1.35 (0.20), residues: 1688 helix: 2.02 (0.17), residues: 898 sheet: 1.24 (0.44), residues: 120 loop : -0.75 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.020 0.002 TYR A1576 PHE 0.019 0.001 PHE A1395 TRP 0.020 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (15097) covalent geometry : angle 0.51266 / 0.28 (20548) hydrogen bonds : bond 0.04750 / 3.16 ( 763) hydrogen bonds : angle 4.04306 / 2.86 ( 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 215 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.507 Fit side-chains REVERT: A 23 LYS cc_start: 0.7935 (tmmt) cc_final: 0.7674 (ttpp) REVERT: A 35 ASP cc_start: 0.6672 (m-30) cc_final: 0.6354 (m-30) REVERT: A 46 ASN cc_start: 0.8310 (m-40) cc_final: 0.7919 (t0) REVERT: A 125 GLU cc_start: 0.8175 (tp30) cc_final: 0.7887 (tp30) REVERT: A 329 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8242 (mmtp) REVERT: A 359 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 487 ASP cc_start: 0.8528 (m-30) cc_final: 0.8256 (m-30) REVERT: A 566 LYS cc_start: 0.8772 (tptp) cc_final: 0.8567 (tptp) REVERT: A 597 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7906 (p0) REVERT: A 779 GLU cc_start: 0.8078 (pt0) cc_final: 0.7794 (mp0) REVERT: A 1056 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: A 1258 THR cc_start: 0.8999 (m) cc_final: 0.8651 (m) REVERT: A 1262 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: A 1469 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: A 1601 ARG cc_start: 0.8339 (ptp-110) cc_final: 0.8042 (ppp80) REVERT: A 1634 ASN cc_start: 0.8636 (t0) cc_final: 0.8384 (t0) REVERT: A 1665 MET cc_start: 0.9358 (OUTLIER) cc_final: 0.9110 (ttt) REVERT: A 1734 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8432 (pp20) outliers start: 23 outliers final: 11 residues processed: 205 average time/residue: 0.5783 time to fit residues: 128.9903 Evaluate side-chains 206 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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 1469 GLU Chi-restraints excluded: chain A residue 1478 MET Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET 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: 0.9980 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.115136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.090142 restraints weight = 17950.673| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.26 r_work: 0.2701 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15097 Z= 0.137 Angle : 0.488 8.433 20548 Z= 0.261 Chirality : 0.040 0.267 2312 Planarity : 0.004 0.040 2461 Dihedral : 7.383 88.953 2294 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.78 % Allowed : 11.51 % 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: 1.48 (0.20), residues: 1688 helix: 2.12 (0.17), residues: 899 sheet: 1.26 (0.45), residues: 120 loop : -0.69 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1017 TYR 0.018 0.001 TYR A1576 PHE 0.018 0.001 PHE A1395 TRP 0.020 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15097) covalent geometry : angle 0.48763 / 0.26 (20548) hydrogen bonds : bond 0.04291 / 2.85 ( 763) hydrogen bonds : angle 3.94589 / 2.80 ( 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 218 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.591 Fit side-chains REVERT: A 35 ASP cc_start: 0.6638 (m-30) cc_final: 0.6315 (m-30) REVERT: A 46 ASN cc_start: 0.8290 (m-40) cc_final: 0.7901 (t0) REVERT: A 125 GLU cc_start: 0.8146 (tp30) cc_final: 0.7853 (tp30) REVERT: A 329 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8214 (mmtp) REVERT: A 359 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: A 487 ASP cc_start: 0.8493 (m-30) cc_final: 0.8217 (m-30) REVERT: A 566 LYS cc_start: 0.8726 (tptp) cc_final: 0.8518 (tptp) REVERT: A 597 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 779 GLU cc_start: 0.7958 (pt0) cc_final: 0.7750 (mp0) REVERT: A 995 ASP cc_start: 0.7818 (m-30) cc_final: 0.7539 (m-30) REVERT: A 1017 ARG cc_start: 0.7389 (mtp-110) cc_final: 0.6837 (mtm180) REVERT: A 1056 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: A 1258 THR cc_start: 0.8970 (m) cc_final: 0.8630 (m) REVERT: A 1262 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6983 (m-30) REVERT: A 1365 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8476 (m) REVERT: A 1469 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: A 1601 ARG cc_start: 0.8336 (ptp-110) cc_final: 0.8043 (ppp80) REVERT: A 1634 ASN cc_start: 0.8624 (t0) cc_final: 0.8385 (t0) REVERT: A 1665 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.9130 (ttt) REVERT: A 1734 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8441 (pp20) outliers start: 28 outliers final: 10 residues processed: 209 average time/residue: 0.6958 time to fit residues: 158.7424 Evaluate side-chains 199 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 496 MET 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 997 LYS Chi-restraints excluded: chain A residue 1056 GLU 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 1466 GLU Chi-restraints excluded: chain A residue 1469 GLU Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1734 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.116579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.091945 restraints weight = 17596.568| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.23 r_work: 0.2722 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15097 Z= 0.118 Angle : 0.468 8.424 20548 Z= 0.251 Chirality : 0.039 0.184 2312 Planarity : 0.003 0.038 2461 Dihedral : 7.287 88.667 2294 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.84 % Allowed : 11.58 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.21), residues: 1688 helix: 2.20 (0.17), residues: 899 sheet: 1.31 (0.45), residues: 120 loop : -0.66 (0.23), residues: 669 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 0.020 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15097) covalent geometry : angle 0.46839 / 0.25 (20548) hydrogen bonds : bond 0.04016 / 2.66 ( 763) hydrogen bonds : angle 3.87361 / 2.74 ( 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 216 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.633 Fit side-chains REVERT: A 35 ASP cc_start: 0.6565 (m-30) cc_final: 0.6239 (m-30) REVERT: A 46 ASN cc_start: 0.8259 (m-40) cc_final: 0.7887 (t0) REVERT: A 125 GLU cc_start: 0.8124 (tp30) cc_final: 0.7858 (tp30) REVERT: A 329 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8248 (mmtp) REVERT: A 359 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: A 487 ASP cc_start: 0.8478 (m-30) cc_final: 0.8201 (m-30) REVERT: A 597 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7817 (p0) REVERT: A 995 ASP cc_start: 0.7755 (m-30) cc_final: 0.7442 (m-30) REVERT: A 1017 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.6877 (mtm180) REVERT: A 1056 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: A 1258 THR cc_start: 0.8963 (m) cc_final: 0.8634 (m) REVERT: A 1262 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: A 1365 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8429 (m) REVERT: A 1601 ARG cc_start: 0.8312 (ptp-110) cc_final: 0.8039 (ppp80) REVERT: A 1634 ASN cc_start: 0.8617 (t0) cc_final: 0.8365 (t0) REVERT: A 1665 MET cc_start: 0.9358 (ttm) cc_final: 0.9111 (ttt) REVERT: A 1734 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8428 (pp20) outliers start: 29 outliers final: 10 residues processed: 206 average time/residue: 0.6875 time to fit residues: 154.5163 Evaluate side-chains 194 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 496 MET Chi-restraints excluded: chain A residue 597 ASP 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 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 1734 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 42 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.089741 restraints weight = 19168.726| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.40 r_work: 0.2705 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15097 Z= 0.136 Angle : 0.485 9.271 20548 Z= 0.260 Chirality : 0.040 0.267 2312 Planarity : 0.004 0.036 2461 Dihedral : 7.314 88.388 2294 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.59 % Allowed : 12.02 % Favored : 86.39 % 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: 1.52 (0.20), residues: 1688 helix: 2.16 (0.17), residues: 898 sheet: 1.39 (0.44), residues: 126 loop : -0.72 (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 0.018 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 0.00317 / 0.14 (15097) covalent geometry : angle 0.48543 / 0.26 (20548) hydrogen bonds : bond 0.04219 / 2.80 ( 763) hydrogen bonds : angle 3.89925 / 2.76 ( 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 207 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.605 Fit side-chains REVERT: A 35 ASP cc_start: 0.6522 (m-30) cc_final: 0.6204 (m-30) REVERT: A 46 ASN cc_start: 0.8267 (m-40) cc_final: 0.7897 (t0) REVERT: A 125 GLU cc_start: 0.8106 (tp30) cc_final: 0.7797 (tp30) REVERT: A 329 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8207 (mmtp) REVERT: A 359 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 487 ASP cc_start: 0.8496 (m-30) cc_final: 0.8216 (m-30) REVERT: A 597 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 995 ASP cc_start: 0.7735 (m-30) cc_final: 0.7400 (m-30) REVERT: A 1017 ARG cc_start: 0.7366 (mtp-110) cc_final: 0.6856 (mtm180) REVERT: A 1056 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: A 1080 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8486 (t0) REVERT: A 1258 THR cc_start: 0.8975 (m) cc_final: 0.8656 (m) REVERT: A 1262 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: A 1365 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8453 (m) REVERT: A 1601 ARG cc_start: 0.8301 (ptp-110) cc_final: 0.8014 (ppp80) REVERT: A 1634 ASN cc_start: 0.8620 (t0) cc_final: 0.8344 (t0) REVERT: A 1665 MET cc_start: 0.9343 (ttm) cc_final: 0.9110 (ttt) REVERT: A 1734 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8428 (pp20) outliers start: 25 outliers final: 10 residues processed: 199 average time/residue: 0.6707 time to fit residues: 146.2146 Evaluate side-chains 198 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 956 LYS 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 1734 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 44 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090408 restraints weight = 19037.599| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.37 r_work: 0.2714 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15097 Z= 0.135 Angle : 0.484 9.510 20548 Z= 0.259 Chirality : 0.040 0.271 2312 Planarity : 0.003 0.040 2461 Dihedral : 7.327 88.449 2294 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.46 % Allowed : 12.47 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.20), residues: 1688 helix: 2.17 (0.17), residues: 898 sheet: 1.38 (0.44), residues: 126 loop : -0.72 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.017 0.001 TYR A1576 PHE 0.018 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 0.00316 / 0.14 (15097) covalent geometry : angle 0.48364 / 0.26 (20548) hydrogen bonds : bond 0.04205 / 2.79 ( 763) hydrogen bonds : angle 3.89881 / 2.76 ( 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 205 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.624 Fit side-chains REVERT: A 35 ASP cc_start: 0.6509 (m-30) cc_final: 0.6192 (m-30) REVERT: A 46 ASN cc_start: 0.8244 (m-40) cc_final: 0.7877 (t0) REVERT: A 125 GLU cc_start: 0.8101 (tp30) cc_final: 0.7798 (tp30) REVERT: A 329 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8202 (mmtp) REVERT: A 359 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: A 487 ASP cc_start: 0.8485 (m-30) cc_final: 0.8226 (m-30) REVERT: A 597 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7818 (p0) REVERT: A 1056 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8043 (mm-30) REVERT: A 1080 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8430 (t0) REVERT: A 1258 THR cc_start: 0.8982 (m) cc_final: 0.8669 (m) REVERT: A 1262 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7039 (m-30) REVERT: A 1365 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 1509 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: A 1601 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.8018 (ppp80) REVERT: A 1634 ASN cc_start: 0.8623 (t0) cc_final: 0.8338 (t0) REVERT: A 1665 MET cc_start: 0.9337 (ttm) cc_final: 0.9115 (ttt) REVERT: A 1734 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8392 (pp20) outliers start: 23 outliers final: 10 residues processed: 199 average time/residue: 0.6924 time to fit residues: 150.9867 Evaluate side-chains 198 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 956 LYS 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 1509 GLU Chi-restraints excluded: chain A residue 1609 THR 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: 0.4980 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 108 optimal weight: 0.0020 chunk 93 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.116833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.090791 restraints weight = 22100.918| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.46 r_work: 0.2727 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15097 Z= 0.112 Angle : 0.469 9.064 20548 Z= 0.250 Chirality : 0.039 0.266 2312 Planarity : 0.004 0.060 2461 Dihedral : 7.243 88.265 2294 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.27 % Allowed : 12.79 % Favored : 85.94 % 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: 1.62 (0.21), residues: 1688 helix: 2.24 (0.17), residues: 899 sheet: 1.46 (0.46), residues: 117 loop : -0.65 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1017 TYR 0.014 0.001 TYR A1576 PHE 0.018 0.001 PHE A1395 TRP 0.020 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (15097) covalent geometry : angle 0.46944 / 0.25 (20548) hydrogen bonds : bond 0.03893 / 2.58 ( 763) hydrogen bonds : angle 3.83144 / 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 200 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.599 Fit side-chains REVERT: A 35 ASP cc_start: 0.6553 (m-30) cc_final: 0.6256 (m-30) REVERT: A 46 ASN cc_start: 0.8240 (m-40) cc_final: 0.7887 (t0) REVERT: A 125 GLU cc_start: 0.8128 (tp30) cc_final: 0.7855 (tp30) REVERT: A 329 LYS cc_start: 0.8513 (mtmt) cc_final: 0.8259 (mmtp) REVERT: A 359 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 487 ASP cc_start: 0.8508 (m-30) cc_final: 0.8253 (m-30) REVERT: A 597 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7797 (p0) REVERT: A 1017 ARG cc_start: 0.7355 (mtp-110) cc_final: 0.6868 (mtm180) REVERT: A 1056 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: A 1080 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8465 (t0) REVERT: A 1258 THR cc_start: 0.8977 (m) cc_final: 0.8733 (m) REVERT: A 1365 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8420 (m) REVERT: A 1509 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: A 1601 ARG cc_start: 0.8322 (ptp-110) cc_final: 0.8045 (ppp80) REVERT: A 1634 ASN cc_start: 0.8607 (t0) cc_final: 0.8331 (t0) REVERT: A 1665 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.9128 (ttt) outliers start: 20 outliers final: 6 residues processed: 195 average time/residue: 0.6763 time to fit residues: 144.1700 Evaluate side-chains 191 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP 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 1509 GLU Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 146 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 169 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3243 r_free = 0.3243 target = 0.116583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.090415 restraints weight = 22791.056| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.48 r_work: 0.2720 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15097 Z= 0.121 Angle : 0.471 8.394 20548 Z= 0.252 Chirality : 0.039 0.169 2312 Planarity : 0.004 0.061 2461 Dihedral : 7.230 87.958 2294 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.08 % Allowed : 13.10 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.23 (0.17), residues: 899 sheet: 1.43 (0.44), residues: 126 loop : -0.68 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1017 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 0.00278 / 0.12 (15097) covalent geometry : angle 0.47088 / 0.25 (20548) hydrogen bonds : bond 0.03981 / 2.64 ( 763) hydrogen bonds : angle 3.83875 / 2.72 ( 2206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.07 seconds wall clock time: 97 minutes 24.70 seconds (5844.70 seconds total)