Starting phenix.real_space_refine on Tue Dec 31 09:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7orn_13043/12_2024/7orn_13043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7orn_13043/12_2024/7orn_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_13043/12_2024/7orn_13043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7orn_13043/12_2024/7orn_13043.map" model { file = "/net/cci-nas-00/data/ceres_data/7orn_13043/12_2024/7orn_13043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7orn_13043/12_2024/7orn_13043.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.42, per 1000 atoms: 0.64 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: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 5.89 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: 8.05 Time building geometry restraints manager: 4.51 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: 8442 17.69 - 35.39: 634 35.39 - 53.08: 123 53.08 - 70.77: 67 70.77 - 88.46: 15 Dihedral angle restraints: 9281 sinusoidal: 4220 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 9278 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: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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= 0.239 Angle : 0.592 12.461 20548 Z= 0.372 Chirality : 0.044 0.329 2312 Planarity : 0.004 0.042 2461 Dihedral : 14.139 88.463 5995 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.035 0.001 TRP A1143 HIS 0.004 0.001 HIS A 814 PHE 0.019 0.001 PHE A1395 TYR 0.018 0.001 TYR A1442 ARG 0.004 0.000 ARG A 144 *********************** 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 : 1.783 Fit side-chains REVERT: A 35 ASP cc_start: 0.6258 (m-30) cc_final: 0.6032 (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: 0.8479 (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: 1.6210 time to fit residues: 409.7607 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 : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 289 GLN A 424 HIS A 497 HIS A1620 HIS A1658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15097 Z= 0.183 Angle : 0.491 8.368 20548 Z= 0.264 Chirality : 0.040 0.228 2312 Planarity : 0.004 0.038 2461 Dihedral : 12.156 85.916 2445 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.02 % Allowed : 7.76 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1688 helix: 2.05 (0.18), residues: 899 sheet: 1.40 (0.44), residues: 129 loop : -0.62 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1143 HIS 0.010 0.001 HIS A1620 PHE 0.019 0.001 PHE A1395 TYR 0.016 0.001 TYR A1576 ARG 0.007 0.000 ARG A1017 *********************** 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 213 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.723 Fit side-chains REVERT: A 487 ASP cc_start: 0.7489 (m-30) cc_final: 0.7162 (m-30) REVERT: A 597 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7398 (p0) REVERT: A 1017 ARG cc_start: 0.7376 (mtp-110) cc_final: 0.7123 (mtm180) REVERT: A 1258 THR cc_start: 0.8768 (m) cc_final: 0.8481 (m) REVERT: A 1262 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6391 (m-30) REVERT: A 1665 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8968 (ttt) outliers start: 16 outliers final: 5 residues processed: 207 average time/residue: 1.5932 time to fit residues: 359.2752 Evaluate side-chains 185 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 106 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A1620 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15097 Z= 0.160 Angle : 0.456 8.207 20548 Z= 0.245 Chirality : 0.039 0.240 2312 Planarity : 0.003 0.031 2461 Dihedral : 12.048 86.384 2445 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.27 % Allowed : 9.22 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1688 helix: 2.19 (0.18), residues: 901 sheet: 1.42 (0.44), residues: 129 loop : -0.65 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.014 0.001 TYR A1576 ARG 0.008 0.000 ARG A 136 *********************** 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 206 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.855 Fit side-chains REVERT: A 487 ASP cc_start: 0.7478 (m-30) cc_final: 0.7160 (m-30) REVERT: A 597 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7366 (p0) REVERT: A 1258 THR cc_start: 0.8724 (m) cc_final: 0.8510 (m) REVERT: A 1612 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 1665 MET cc_start: 0.9180 (ttm) cc_final: 0.8954 (ttt) REVERT: A 1734 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7868 (pp20) outliers start: 20 outliers final: 6 residues processed: 198 average time/residue: 1.5695 time to fit residues: 339.9221 Evaluate side-chains 187 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 997 LYS Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1606 SER 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 154 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 0.0010 chunk 44 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 46 ASN A 159 ASN A 332 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15097 Z= 0.161 Angle : 0.452 8.278 20548 Z= 0.243 Chirality : 0.039 0.255 2312 Planarity : 0.003 0.032 2461 Dihedral : 11.998 87.180 2445 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.46 % Allowed : 10.31 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.21), residues: 1688 helix: 2.26 (0.18), residues: 901 sheet: 1.44 (0.44), residues: 129 loop : -0.63 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.012 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.016 0.001 TYR A1576 ARG 0.010 0.000 ARG A1017 *********************** 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 208 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 487 ASP cc_start: 0.7483 (m-30) cc_final: 0.7183 (m-30) REVERT: A 597 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7365 (p0) REVERT: A 1056 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: A 1080 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7888 (t0) REVERT: A 1612 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 1665 MET cc_start: 0.9176 (ttm) cc_final: 0.8944 (ttt) outliers start: 23 outliers final: 7 residues processed: 200 average time/residue: 1.4842 time to fit residues: 325.0567 Evaluate side-chains 183 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN A 506 GLN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15097 Z= 0.379 Angle : 0.572 8.393 20548 Z= 0.307 Chirality : 0.044 0.196 2312 Planarity : 0.004 0.055 2461 Dihedral : 12.531 89.052 2445 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.46 % Allowed : 11.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.20), residues: 1688 helix: 1.94 (0.17), residues: 898 sheet: 1.32 (0.45), residues: 120 loop : -0.80 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1143 HIS 0.012 0.001 HIS A1620 PHE 0.020 0.002 PHE A1395 TYR 0.022 0.002 TYR A1576 ARG 0.008 0.001 ARG A 136 *********************** 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 208 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.638 Fit side-chains REVERT: A 487 ASP cc_start: 0.7529 (m-30) cc_final: 0.7238 (m-30) REVERT: A 597 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7598 (p0) REVERT: A 1056 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: A 1262 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.6260 (m-30) outliers start: 23 outliers final: 8 residues processed: 199 average time/residue: 1.5548 time to fit residues: 338.2220 Evaluate side-chains 188 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 732 PHE Chi-restraints excluded: chain A residue 956 LYS Chi-restraints excluded: chain A residue 988 GLU 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 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.0370 chunk 149 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN A 332 GLN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15097 Z= 0.171 Angle : 0.475 8.449 20548 Z= 0.255 Chirality : 0.040 0.255 2312 Planarity : 0.003 0.033 2461 Dihedral : 12.278 89.660 2445 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1688 helix: 2.13 (0.17), residues: 898 sheet: 1.32 (0.45), residues: 120 loop : -0.70 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.016 0.001 TYR A1576 ARG 0.007 0.000 ARG A 136 *********************** 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 202 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.660 Fit side-chains REVERT: A 487 ASP cc_start: 0.7482 (m-30) cc_final: 0.7195 (m-30) REVERT: A 597 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7471 (p0) REVERT: A 1056 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: A 1262 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6182 (m-30) REVERT: A 1365 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (m) REVERT: A 1665 MET cc_start: 0.9179 (ttm) cc_final: 0.8959 (ttt) outliers start: 25 outliers final: 9 residues processed: 193 average time/residue: 1.5526 time to fit residues: 327.8981 Evaluate side-chains 184 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1657 GLU Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1459 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= 0.185 Angle : 0.476 8.952 20548 Z= 0.255 Chirality : 0.040 0.263 2312 Planarity : 0.003 0.034 2461 Dihedral : 12.219 88.937 2445 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.59 % Allowed : 12.09 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.20), residues: 1688 helix: 2.18 (0.17), residues: 899 sheet: 1.36 (0.45), residues: 120 loop : -0.68 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.011 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.016 0.001 TYR A1576 ARG 0.008 0.000 ARG A 136 *********************** 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 200 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.716 Fit side-chains REVERT: A 487 ASP cc_start: 0.7486 (m-30) cc_final: 0.7192 (m-30) REVERT: A 597 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7473 (p0) REVERT: A 1056 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: A 1262 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6156 (m-30) REVERT: A 1365 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8162 (m) REVERT: A 1665 MET cc_start: 0.9181 (ttm) cc_final: 0.8971 (ttt) outliers start: 25 outliers final: 10 residues processed: 193 average time/residue: 1.5159 time to fit residues: 320.6197 Evaluate side-chains 186 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1606 SER Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN A 523 GLN A1007 GLN A1620 HIS A1634 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15097 Z= 0.233 Angle : 0.498 9.383 20548 Z= 0.267 Chirality : 0.041 0.272 2312 Planarity : 0.004 0.036 2461 Dihedral : 12.286 88.978 2445 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.34 % Allowed : 12.53 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1688 helix: 2.13 (0.17), residues: 898 sheet: 1.47 (0.45), residues: 117 loop : -0.72 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.008 0.000 ARG A 136 *********************** 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 200 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.587 Fit side-chains REVERT: A 487 ASP cc_start: 0.7506 (m-30) cc_final: 0.7240 (m-30) REVERT: A 597 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7502 (p0) REVERT: A 1056 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: A 1262 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6177 (m-30) REVERT: A 1365 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8247 (m) REVERT: A 1581 ASP cc_start: 0.8013 (t0) cc_final: 0.7808 (t70) REVERT: A 1665 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8976 (ttt) outliers start: 21 outliers final: 10 residues processed: 191 average time/residue: 1.5313 time to fit residues: 320.2771 Evaluate side-chains 188 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 159 ASN A 523 GLN A1007 GLN A1620 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.004 0.046 15097 Z= 0.241 Angle : 0.506 9.526 20548 Z= 0.271 Chirality : 0.041 0.274 2312 Planarity : 0.004 0.037 2461 Dihedral : 12.330 89.244 2445 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.34 % Allowed : 12.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1688 helix: 2.11 (0.17), residues: 898 sheet: 1.47 (0.45), residues: 117 loop : -0.73 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.013 0.001 HIS A1620 PHE 0.019 0.001 PHE A1395 TYR 0.019 0.001 TYR A1576 ARG 0.008 0.000 ARG A 136 *********************** 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 195 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.627 Fit side-chains REVERT: A 487 ASP cc_start: 0.7503 (m-30) cc_final: 0.7226 (m-30) REVERT: A 597 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7528 (p0) REVERT: A 758 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: A 1056 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: A 1262 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6205 (m-30) REVERT: A 1365 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8262 (m) REVERT: A 1665 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8955 (ttt) outliers start: 21 outliers final: 11 residues processed: 187 average time/residue: 1.5339 time to fit residues: 314.1928 Evaluate side-chains 187 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 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 1665 MET Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A1007 GLN A1620 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1534 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= 0.226 Angle : 0.498 8.972 20548 Z= 0.267 Chirality : 0.040 0.171 2312 Planarity : 0.004 0.040 2461 Dihedral : 12.315 89.336 2445 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.21 % Allowed : 12.60 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1688 helix: 2.13 (0.17), residues: 898 sheet: 1.48 (0.45), residues: 123 loop : -0.73 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1143 HIS 0.014 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.018 0.001 TYR A1576 ARG 0.008 0.000 ARG A 136 ********************** 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 192 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.641 Fit side-chains REVERT: A 487 ASP cc_start: 0.7501 (m-30) cc_final: 0.7227 (m-30) REVERT: A 597 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7518 (p0) REVERT: A 758 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: A 1056 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: A 1262 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.6229 (m-30) REVERT: A 1365 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8248 (m) REVERT: A 1665 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8968 (ttt) outliers start: 19 outliers final: 10 residues processed: 184 average time/residue: 1.4508 time to fit residues: 293.1895 Evaluate side-chains 186 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 621 ASP Chi-restraints excluded: chain A residue 758 GLU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 997 LYS Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1238 PHE Chi-restraints excluded: chain A residue 1262 ASP Chi-restraints excluded: chain A residue 1365 THR Chi-restraints excluded: chain A residue 1609 THR Chi-restraints excluded: chain A residue 1665 MET Chi-restraints excluded: chain A residue 1725 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3233 r_free = 0.3233 target = 0.115996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090316 restraints weight = 19299.198| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.35 r_work: 0.2721 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1570 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= 0.174 Angle : 0.472 8.447 20548 Z= 0.253 Chirality : 0.039 0.302 2312 Planarity : 0.003 0.038 2461 Dihedral : 12.203 89.066 2445 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.08 % Allowed : 12.66 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1688 helix: 2.21 (0.17), residues: 899 sheet: 1.53 (0.46), residues: 117 loop : -0.65 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1143 HIS 0.014 0.001 HIS A1620 PHE 0.018 0.001 PHE A1395 TYR 0.015 0.001 TYR A 6 ARG 0.008 0.000 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5985.53 seconds wall clock time: 108 minutes 23.59 seconds (6503.59 seconds total)