Starting phenix.real_space_refine on Thu Jul 2 23:21:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7r_33046/07_2026/7x7r_33046.cif" } resolution = 3.5 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= 1.000 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 Zn 4 6.06 5 P 56 5.49 5 S 31 5.16 5 C 6510 2.51 5 N 1854 2.21 5 O 2074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 10529 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 758 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "J" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 436 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "A" Number of atoms: 9331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1237, 9331 Classifications: {'peptide': 1237} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 59, 'TRANS': 1177} Chain breaks: 9 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 42, 'ASN:plan1': 19, 'GLN:plan1': 9, 'ASP:plan': 25, 'HIS:plan': 3, 'ARG:plan': 9, 'PHE:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 427 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4549 SG CYS A 491 21.330 25.347 102.757 1.00 39.67 S ATOM 4631 SG CYS A 503 21.864 25.027 104.149 1.00 40.30 S ATOM 4653 SG CYS A 506 24.237 26.584 103.898 1.00 34.60 S ATOM 1852 SG CYS A 88 28.779 35.019 134.217 1.00 54.56 S ATOM 2090 SG CYS A 121 27.754 36.202 137.716 1.00 80.87 S ATOM 2121 SG CYS A 127 31.434 36.295 136.707 1.00 63.26 S ATOM 2145 SG CYS A 130 28.979 38.632 135.016 1.00 57.48 S ATOM 6514 SG CYS A 750 12.128 24.187 73.080 1.00 80.94 S ATOM 6527 SG CYS A 752 15.322 22.825 71.640 1.00 66.35 S ATOM 6549 SG CYS A 755 15.557 24.790 74.873 1.00 52.19 S ATOM 8530 SG CYS A1406 19.111 40.825 43.697 1.00 53.55 S ATOM 8581 SG CYS A1414 18.032 40.581 41.695 1.00 43.81 S ATOM 8598 SG CYS A1417 21.390 39.108 43.424 1.00 39.10 S Time building chain proxies: 2.46, per 1000 atoms: 0.23 Number of scatterers: 10529 At special positions: 0 Unit cell: (73.1499, 84.5499, 152, 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) Zn 4 29.99 S 31 16.00 P 56 15.00 O 2074 8.00 N 1854 7.00 C 6510 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: 0.89 Conformation dependent library (CDL) restraints added in 363.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 9 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 29.0% alpha, 15.0% beta 5 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.282A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.011A pdb=" N MET A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.516A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.648A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.677A pdb=" N ILE A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.276A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.761A pdb=" N ARG A 510 " --> pdb=" O CYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 removed outlier: 3.795A pdb=" N ARG A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.577A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.999A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.820A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 removed outlier: 3.567A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.791A pdb=" N LYS A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.527A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.508A pdb=" N ILE A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.515A pdb=" N VAL A 858 " --> pdb=" O LYS A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.824A pdb=" N GLU A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.741A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.823A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 removed outlier: 3.500A pdb=" N LEU A1419 " --> pdb=" O PRO A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.341A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.801A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1499 Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.847A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A1534 " --> pdb=" O TRP A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1599 removed outlier: 4.103A pdb=" N GLY A1594 " --> pdb=" O TYR A1590 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A1599 " --> pdb=" O TYR A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.602A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 removed outlier: 3.815A pdb=" N LYS A1624 " --> pdb=" O PRO A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.661A pdb=" N VAL A1678 " --> pdb=" O TYR A1674 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A1679 " --> pdb=" O LYS A1675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 158 removed outlier: 5.527A pdb=" N PHE A 153 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR A 210 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN A 155 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 208 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 238 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.012A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.889A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 513 removed outlier: 6.732A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 534 removed outlier: 5.884A pdb=" N SER A 544 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N ASN A 534 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N ASP A 542 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.823A pdb=" N ARG A 768 " --> pdb=" O TRP A 825 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.627A pdb=" N GLU A 677 " --> pdb=" O GLY A 865 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY A 865 " --> pdb=" O GLU A 677 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 925 through 927 Processing sheet with id=AB2, first strand: chain 'A' and resid 950 through 952 removed outlier: 7.224A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1430 through 1431 removed outlier: 6.773A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 985 through 986 removed outlier: 6.201A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 991 through 992 277 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2879 1.33 - 1.45: 2252 1.45 - 1.57: 5606 1.57 - 1.69: 110 1.69 - 1.81: 42 Bond restraints: 10889 Sorted by residual: bond pdb=" N1 C J 23 " pdb=" C2 C J 23 " ideal model delta sigma weight residual 1.397 1.419 -0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C3' A J 19 " pdb=" O3' A J 19 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" N PHE A 24 " pdb=" CA PHE A 24 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.88e-01 bond pdb=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 1.607 1.618 -0.011 1.50e-02 4.44e+03 5.51e-01 bond pdb=" N ASP A 400 " pdb=" CA ASP A 400 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.54e-02 4.22e+03 5.40e-01 ... (remaining 10884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14689 1.66 - 3.33: 277 3.33 - 4.99: 54 4.99 - 6.65: 11 6.65 - 8.32: 5 Bond angle restraints: 15036 Sorted by residual: angle pdb=" C3' A J 19 " pdb=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 120.20 125.16 -4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" N VAL A1618 " pdb=" CA VAL A1618 " pdb=" C VAL A1618 " ideal model delta sigma weight residual 112.29 109.52 2.77 9.40e-01 1.13e+00 8.68e+00 angle pdb=" C1' C J 23 " pdb=" N1 C J 23 " pdb=" C2 C J 23 " ideal model delta sigma weight residual 118.80 127.12 -8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" C PHE A 780 " pdb=" N GLU A 781 " pdb=" CA GLU A 781 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.63e+00 angle pdb=" C PHE A 24 " pdb=" CA PHE A 24 " pdb=" CB PHE A 24 " ideal model delta sigma weight residual 110.42 115.78 -5.36 1.99e+00 2.53e-01 7.26e+00 ... (remaining 15031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 6105 35.18 - 70.36: 164 70.36 - 105.53: 18 105.53 - 140.71: 0 140.71 - 175.89: 5 Dihedral angle restraints: 6292 sinusoidal: 2764 harmonic: 3528 Sorted by residual: dihedral pdb=" O4' U C -14 " pdb=" C1' U C -14 " pdb=" N1 U C -14 " pdb=" C2 U C -14 " ideal model delta sinusoidal sigma weight residual 200.00 58.81 141.19 1 1.50e+01 4.44e-03 7.59e+01 dihedral pdb=" O4' U J 36 " pdb=" C1' U J 36 " pdb=" N1 U J 36 " pdb=" C2 U J 36 " ideal model delta sinusoidal sigma weight residual 232.00 56.11 175.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual -128.00 47.38 -175.38 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 6289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1363 0.046 - 0.091: 262 0.091 - 0.137: 70 0.137 - 0.182: 5 0.182 - 0.228: 1 Chirality restraints: 1701 Sorted by residual: chirality pdb=" CB ILE A1468 " pdb=" CA ILE A1468 " pdb=" CG1 ILE A1468 " pdb=" CG2 ILE A1468 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' A J 19 " pdb=" C4' A J 19 " pdb=" O3' A J 19 " pdb=" C2' A J 19 " both_signs ideal model delta sigma weight residual False -2.74 -2.58 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" C1' U C -14 " pdb=" O4' U C -14 " pdb=" C2' U C -14 " pdb=" N1 U C -14 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1698 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1475 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A1476 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1476 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1476 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 316 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 317 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 1 " 0.017 2.00e-02 2.50e+03 9.94e-03 2.22e+00 pdb=" N1 C C 1 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C C 1 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C C 1 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C C 1 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C C 1 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C C 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C C 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C C 1 " -0.001 2.00e-02 2.50e+03 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 154 2.63 - 3.19: 9366 3.19 - 3.76: 16766 3.76 - 4.33: 22090 4.33 - 4.90: 35754 Nonbonded interactions: 84130 Sorted by model distance: nonbonded pdb=" O2' U C 5 " pdb=" O ALA A 685 " model vdw 2.058 3.040 nonbonded pdb=" O LEU A1648 " pdb=" OG1 THR A1662 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 680 " pdb=" O GLY A 859 " model vdw 2.263 3.040 nonbonded pdb=" O2' G J 20 " pdb=" O4' U J 21 " model vdw 2.263 3.040 nonbonded pdb=" NH2 ARG A 737 " pdb=" OE1 GLU A1525 " model vdw 2.264 3.120 ... (remaining 84125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.730 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 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 : 0.002 0.035 10903 Z= 0.100 Angle : 0.587 8.316 15045 Z= 0.291 Chirality : 0.040 0.228 1701 Planarity : 0.003 0.043 1726 Dihedral : 16.465 175.890 4032 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.19 (0.25), residues: 1217 helix: 0.20 (0.32), residues: 292 sheet: -0.80 (0.42), residues: 170 loop : -1.22 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 19 TYR 0.018 0.001 TYR A 649 PHE 0.023 0.001 PHE A 546 TRP 0.015 0.001 TRP A 862 HIS 0.004 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (10889) covalent geometry : angle 0.58426 / 0.29 (15036) hydrogen bonds : bond 0.19878 / 11.61 ( 278) hydrogen bonds : angle 8.62184 / 4.82 ( 796) metal coordination : bond 0.00317 / 0.21 ( 14) metal coordination : angle 2.35710 / 0.79 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.6243 (tmm) cc_final: 0.5741 (tmm) REVERT: A 191 TYR cc_start: 0.6919 (p90) cc_final: 0.6715 (p90) REVERT: A 627 MET cc_start: 0.7202 (mtt) cc_final: 0.6970 (mtt) REVERT: A 760 ASN cc_start: 0.7368 (p0) cc_final: 0.7139 (p0) REVERT: A 1004 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7185 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1098 time to fit residues: 25.2214 Evaluate side-chains 114 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.191443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.152125 restraints weight = 14519.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.158548 restraints weight = 7661.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162803 restraints weight = 5122.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.165600 restraints weight = 3935.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167478 restraints weight = 3298.529| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10903 Z= 0.126 Angle : 0.586 8.148 15045 Z= 0.294 Chirality : 0.042 0.299 1701 Planarity : 0.004 0.044 1726 Dihedral : 15.361 176.185 1996 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.33 % Allowed : 10.56 % Favored : 88.11 % 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: -1.38 (0.24), residues: 1217 helix: 0.03 (0.30), residues: 308 sheet: -0.97 (0.40), residues: 176 loop : -1.34 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 356 TYR 0.022 0.002 TYR A 199 PHE 0.020 0.001 PHE A 824 TRP 0.008 0.001 TRP A 44 HIS 0.005 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10889) covalent geometry : angle 0.57937 / 0.29 (15036) hydrogen bonds : bond 0.03895 / 2.34 ( 278) hydrogen bonds : angle 6.00967 / 3.34 ( 796) metal coordination : bond 0.00538 / 0.36 ( 14) metal coordination : angle 3.61131 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.359 Fit side-chains REVERT: A 507 ILE cc_start: 0.7897 (mt) cc_final: 0.7268 (pt) REVERT: A 526 GLU cc_start: 0.7533 (pt0) cc_final: 0.7118 (pt0) REVERT: A 564 ARG cc_start: 0.5455 (ttm170) cc_final: 0.4889 (mtt-85) REVERT: A 624 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7849 (tt0) REVERT: A 760 ASN cc_start: 0.7891 (p0) cc_final: 0.7401 (p0) REVERT: A 1004 ARG cc_start: 0.7756 (tpt170) cc_final: 0.7291 (tpp-160) outliers start: 12 outliers final: 7 residues processed: 143 average time/residue: 0.1081 time to fit residues: 21.9782 Evaluate side-chains 127 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 961 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.189897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.149554 restraints weight = 14999.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.156013 restraints weight = 7983.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.160258 restraints weight = 5383.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.163007 restraints weight = 4175.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.164878 restraints weight = 3535.762| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10903 Z= 0.114 Angle : 0.565 11.207 15045 Z= 0.281 Chirality : 0.042 0.315 1701 Planarity : 0.004 0.052 1726 Dihedral : 15.326 175.985 1996 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.33 % Allowed : 15.67 % Favored : 83.00 % 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: -1.30 (0.24), residues: 1217 helix: 0.09 (0.30), residues: 314 sheet: -0.64 (0.42), residues: 169 loop : -1.38 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 168 TYR 0.016 0.001 TYR A 649 PHE 0.018 0.001 PHE A 824 TRP 0.018 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10889) covalent geometry : angle 0.56041 / 0.28 (15036) hydrogen bonds : bond 0.03359 / 2.03 ( 278) hydrogen bonds : angle 5.53293 / 3.09 ( 796) metal coordination : bond 0.00380 / 0.25 ( 14) metal coordination : angle 3.10815 / 1.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.377 Fit side-chains REVERT: A 36 MET cc_start: 0.8342 (mpp) cc_final: 0.8126 (mpp) REVERT: A 504 LYS cc_start: 0.5513 (mmmt) cc_final: 0.5261 (mmmt) REVERT: A 507 ILE cc_start: 0.7818 (mt) cc_final: 0.7202 (pt) REVERT: A 624 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7878 (tt0) REVERT: A 627 MET cc_start: 0.7817 (mtt) cc_final: 0.7540 (mtt) REVERT: A 760 ASN cc_start: 0.7832 (p0) cc_final: 0.7309 (p0) outliers start: 12 outliers final: 9 residues processed: 140 average time/residue: 0.1099 time to fit residues: 21.8200 Evaluate side-chains 132 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 106 optimal weight: 0.0470 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.189272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.148370 restraints weight = 15288.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.154765 restraints weight = 8179.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.158958 restraints weight = 5567.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.161474 restraints weight = 4358.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.163370 restraints weight = 3736.092| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10903 Z= 0.131 Angle : 0.571 12.275 15045 Z= 0.284 Chirality : 0.042 0.326 1701 Planarity : 0.004 0.054 1726 Dihedral : 15.360 176.849 1996 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.44 % Allowed : 17.89 % Favored : 79.67 % 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: -1.26 (0.25), residues: 1217 helix: 0.23 (0.30), residues: 302 sheet: -0.71 (0.42), residues: 169 loop : -1.36 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.014 0.001 TYR A 649 PHE 0.034 0.001 PHE A 226 TRP 0.020 0.001 TRP A1530 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10889) covalent geometry : angle 0.56621 / 0.28 (15036) hydrogen bonds : bond 0.03270 / 1.98 ( 278) hydrogen bonds : angle 5.29017 / 2.95 ( 796) metal coordination : bond 0.00473 / 0.31 ( 14) metal coordination : angle 3.11719 / 1.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8310 (mpp) cc_final: 0.8063 (mpp) REVERT: A 507 ILE cc_start: 0.7914 (mt) cc_final: 0.7245 (pt) REVERT: A 514 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6227 (pp) REVERT: A 564 ARG cc_start: 0.5682 (ttm170) cc_final: 0.5305 (mtt-85) REVERT: A 624 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7925 (tt0) REVERT: A 627 MET cc_start: 0.7924 (mtt) cc_final: 0.7695 (mtt) REVERT: A 760 ASN cc_start: 0.8014 (p0) cc_final: 0.7472 (p0) REVERT: A 1016 LYS cc_start: 0.8278 (pptt) cc_final: 0.7009 (tptt) outliers start: 22 outliers final: 11 residues processed: 149 average time/residue: 0.1099 time to fit residues: 23.2773 Evaluate side-chains 139 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1562 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 776 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.187087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146627 restraints weight = 14932.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152671 restraints weight = 8215.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.156628 restraints weight = 5671.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.159227 restraints weight = 4482.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.160958 restraints weight = 3837.866| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10903 Z= 0.152 Angle : 0.598 12.967 15045 Z= 0.298 Chirality : 0.042 0.317 1701 Planarity : 0.005 0.072 1726 Dihedral : 15.420 177.741 1996 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.44 % Allowed : 18.44 % Favored : 78.11 % 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: -1.27 (0.25), residues: 1217 helix: 0.22 (0.31), residues: 295 sheet: -0.74 (0.42), residues: 169 loop : -1.35 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.017 0.002 TYR A 199 PHE 0.024 0.001 PHE A 824 TRP 0.021 0.001 TRP A1530 HIS 0.004 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10889) covalent geometry : angle 0.59252 / 0.30 (15036) hydrogen bonds : bond 0.03308 / 2.01 ( 278) hydrogen bonds : angle 5.25469 / 2.94 ( 796) metal coordination : bond 0.00525 / 0.35 ( 14) metal coordination : angle 3.23115 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8300 (mpp) cc_final: 0.8019 (mpp) REVERT: A 507 ILE cc_start: 0.7923 (mt) cc_final: 0.7211 (pt) REVERT: A 514 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6377 (pp) REVERT: A 624 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7964 (tt0) REVERT: A 627 MET cc_start: 0.7964 (mtt) cc_final: 0.7708 (mtt) REVERT: A 719 ARG cc_start: 0.7425 (mpt180) cc_final: 0.7185 (mpt180) REVERT: A 760 ASN cc_start: 0.8105 (p0) cc_final: 0.7532 (p0) REVERT: A 776 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.6143 (p0) REVERT: A 1016 LYS cc_start: 0.8291 (pptt) cc_final: 0.7058 (tptt) outliers start: 31 outliers final: 18 residues processed: 143 average time/residue: 0.1100 time to fit residues: 22.2897 Evaluate side-chains 139 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 776 ASN Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 95 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.187720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147037 restraints weight = 15019.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.153272 restraints weight = 8113.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.157395 restraints weight = 5543.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.160112 restraints weight = 4347.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.161746 restraints weight = 3695.546| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10903 Z= 0.127 Angle : 0.587 13.651 15045 Z= 0.290 Chirality : 0.042 0.331 1701 Planarity : 0.004 0.065 1726 Dihedral : 15.395 178.026 1996 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.56 % Allowed : 20.56 % Favored : 76.89 % 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: -1.28 (0.25), residues: 1217 helix: 0.22 (0.31), residues: 295 sheet: -0.75 (0.42), residues: 169 loop : -1.36 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 168 TYR 0.018 0.002 TYR A 199 PHE 0.022 0.001 PHE A 824 TRP 0.024 0.001 TRP A1530 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10889) covalent geometry : angle 0.58263 / 0.29 (15036) hydrogen bonds : bond 0.03126 / 1.90 ( 278) hydrogen bonds : angle 5.14115 / 2.88 ( 796) metal coordination : bond 0.00387 / 0.25 ( 14) metal coordination : angle 2.99657 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.375 Fit side-chains REVERT: A 36 MET cc_start: 0.8317 (mpp) cc_final: 0.8020 (mpp) REVERT: A 472 ARG cc_start: 0.6818 (tmm-80) cc_final: 0.6602 (tmm160) REVERT: A 514 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6383 (pp) REVERT: A 563 TYR cc_start: 0.7258 (t80) cc_final: 0.6855 (t80) REVERT: A 564 ARG cc_start: 0.5743 (ttm170) cc_final: 0.5534 (mtt-85) REVERT: A 624 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7943 (tt0) REVERT: A 627 MET cc_start: 0.7979 (mtt) cc_final: 0.7675 (mtt) REVERT: A 760 ASN cc_start: 0.8084 (p0) cc_final: 0.7495 (p0) REVERT: A 1004 ARG cc_start: 0.7794 (tpt170) cc_final: 0.7450 (tpt90) REVERT: A 1016 LYS cc_start: 0.8344 (pptt) cc_final: 0.7169 (tptt) REVERT: A 1512 MET cc_start: 0.6919 (mmm) cc_final: 0.6663 (mmm) outliers start: 23 outliers final: 20 residues processed: 143 average time/residue: 0.1139 time to fit residues: 22.9793 Evaluate side-chains 144 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 87 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 924 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.184094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143489 restraints weight = 15133.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.149554 restraints weight = 8239.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.153603 restraints weight = 5662.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.156178 restraints weight = 4448.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.157629 restraints weight = 3805.571| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10903 Z= 0.175 Angle : 0.633 13.488 15045 Z= 0.315 Chirality : 0.043 0.308 1701 Planarity : 0.005 0.062 1726 Dihedral : 15.553 179.489 1996 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 3.67 % Allowed : 20.67 % Favored : 75.67 % 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 (0.25), residues: 1217 helix: 0.14 (0.31), residues: 290 sheet: -0.83 (0.42), residues: 169 loop : -1.44 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 304 TYR 0.019 0.002 TYR A 199 PHE 0.027 0.002 PHE A 824 TRP 0.028 0.002 TRP A1530 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (10889) covalent geometry : angle 0.62670 / 0.31 (15036) hydrogen bonds : bond 0.03458 / 2.11 ( 278) hydrogen bonds : angle 5.23979 / 2.93 ( 796) metal coordination : bond 0.00504 / 0.33 ( 14) metal coordination : angle 3.62956 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.424 Fit side-chains REVERT: A 36 MET cc_start: 0.8360 (mpp) cc_final: 0.8095 (mpp) REVERT: A 563 TYR cc_start: 0.7285 (t80) cc_final: 0.6937 (t80) REVERT: A 564 ARG cc_start: 0.5935 (ttm170) cc_final: 0.5418 (mtt-85) REVERT: A 624 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7909 (tt0) REVERT: A 627 MET cc_start: 0.7990 (mtt) cc_final: 0.7629 (mtt) REVERT: A 1004 ARG cc_start: 0.7861 (tpt170) cc_final: 0.7374 (tpp-160) REVERT: A 1016 LYS cc_start: 0.8343 (pptt) cc_final: 0.7137 (tptt) REVERT: A 1593 LYS cc_start: 0.7322 (mptt) cc_final: 0.6675 (mmmm) outliers start: 33 outliers final: 24 residues processed: 141 average time/residue: 0.1026 time to fit residues: 20.7547 Evaluate side-chains 142 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1591 ILE Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.185215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145771 restraints weight = 14880.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151544 restraints weight = 8368.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.155395 restraints weight = 5847.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.158001 restraints weight = 4629.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.159612 restraints weight = 3946.772| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10903 Z= 0.145 Angle : 0.627 14.221 15045 Z= 0.307 Chirality : 0.042 0.313 1701 Planarity : 0.004 0.070 1726 Dihedral : 15.516 179.245 1996 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.22 % Allowed : 22.67 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.25), residues: 1217 helix: 0.16 (0.31), residues: 290 sheet: -0.91 (0.41), residues: 176 loop : -1.38 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 737 TYR 0.019 0.002 TYR A 199 PHE 0.023 0.001 PHE A 824 TRP 0.029 0.001 TRP A1530 HIS 0.005 0.001 HIS A1418 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10889) covalent geometry : angle 0.61986 / 0.31 (15036) hydrogen bonds : bond 0.03237 / 1.97 ( 278) hydrogen bonds : angle 5.14607 / 2.90 ( 796) metal coordination : bond 0.00440 / 0.29 ( 14) metal coordination : angle 3.83038 / 1.28 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.382 Fit side-chains REVERT: A 36 MET cc_start: 0.8294 (mpp) cc_final: 0.8000 (mpp) REVERT: A 167 LEU cc_start: 0.5573 (OUTLIER) cc_final: 0.5150 (pp) REVERT: A 472 ARG cc_start: 0.7066 (tmm-80) cc_final: 0.6668 (tmm160) REVERT: A 624 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7978 (tt0) REVERT: A 627 MET cc_start: 0.8079 (mtt) cc_final: 0.7687 (mtt) REVERT: A 1016 LYS cc_start: 0.8267 (pptt) cc_final: 0.7202 (tptt) REVERT: A 1593 LYS cc_start: 0.7290 (mptt) cc_final: 0.6680 (mmmm) outliers start: 29 outliers final: 23 residues processed: 138 average time/residue: 0.1101 time to fit residues: 21.4610 Evaluate side-chains 145 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 0.0000 overall best weight: 0.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.189494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149340 restraints weight = 14926.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.155570 restraints weight = 8071.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.159714 restraints weight = 5507.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.162444 restraints weight = 4304.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164116 restraints weight = 3649.023| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10903 Z= 0.103 Angle : 0.601 14.659 15045 Z= 0.292 Chirality : 0.042 0.327 1701 Planarity : 0.004 0.066 1726 Dihedral : 15.363 178.745 1996 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.56 % Allowed : 23.78 % Favored : 73.67 % 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: -1.26 (0.25), residues: 1217 helix: 0.27 (0.31), residues: 290 sheet: -0.72 (0.42), residues: 169 loop : -1.36 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 737 TYR 0.019 0.001 TYR A 199 PHE 0.019 0.001 PHE A 824 TRP 0.032 0.001 TRP A1530 HIS 0.005 0.001 HIS A1418 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (10889) covalent geometry : angle 0.59759 / 0.29 (15036) hydrogen bonds : bond 0.02908 / 1.77 ( 278) hydrogen bonds : angle 4.91409 / 2.79 ( 796) metal coordination : bond 0.00344 / 0.23 ( 14) metal coordination : angle 2.85654 / 0.95 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.313 Fit side-chains REVERT: A 36 MET cc_start: 0.8333 (mpp) cc_final: 0.8013 (mpp) REVERT: A 167 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.5075 (pt) REVERT: A 202 TYR cc_start: 0.6681 (m-80) cc_final: 0.6454 (m-80) REVERT: A 472 ARG cc_start: 0.6763 (tmm-80) cc_final: 0.6529 (tmm160) REVERT: A 624 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7929 (tt0) REVERT: A 627 MET cc_start: 0.8070 (mtt) cc_final: 0.7639 (mtt) REVERT: A 1004 ARG cc_start: 0.7840 (tpt170) cc_final: 0.7536 (tpt90) REVERT: A 1016 LYS cc_start: 0.8314 (pptt) cc_final: 0.7204 (tptt) outliers start: 23 outliers final: 17 residues processed: 143 average time/residue: 0.0910 time to fit residues: 18.6477 Evaluate side-chains 138 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 0.0970 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 466 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.190601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.150808 restraints weight = 14814.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.157071 restraints weight = 7984.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.161271 restraints weight = 5417.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.163959 restraints weight = 4204.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.165484 restraints weight = 3565.394| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6398 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10903 Z= 0.103 Angle : 0.612 14.471 15045 Z= 0.297 Chirality : 0.041 0.316 1701 Planarity : 0.004 0.065 1726 Dihedral : 15.319 178.671 1996 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.22 % Allowed : 24.67 % Favored : 73.11 % 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: -1.24 (0.24), residues: 1217 helix: 0.39 (0.31), residues: 285 sheet: -0.63 (0.42), residues: 169 loop : -1.39 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.020 0.001 TYR A 199 PHE 0.020 0.001 PHE A 824 TRP 0.033 0.001 TRP A1530 HIS 0.006 0.001 HIS A1418 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10889) covalent geometry : angle 0.60828 / 0.30 (15036) hydrogen bonds : bond 0.02869 / 1.74 ( 278) hydrogen bonds : angle 4.83193 / 2.73 ( 796) metal coordination : bond 0.00300 / 0.20 ( 14) metal coordination : angle 2.64352 / 0.88 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.372 Fit side-chains REVERT: A 36 MET cc_start: 0.8336 (mpp) cc_final: 0.8048 (mpp) REVERT: A 167 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5141 (pt) REVERT: A 202 TYR cc_start: 0.6687 (m-80) cc_final: 0.6457 (m-80) REVERT: A 472 ARG cc_start: 0.6702 (tmm-80) cc_final: 0.6487 (tmm160) REVERT: A 563 TYR cc_start: 0.7255 (t80) cc_final: 0.6812 (t80) REVERT: A 624 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7906 (tt0) REVERT: A 627 MET cc_start: 0.8066 (mtt) cc_final: 0.7631 (mtt) REVERT: A 719 ARG cc_start: 0.7491 (mpt180) cc_final: 0.7215 (mpt180) REVERT: A 1004 ARG cc_start: 0.7771 (tpt170) cc_final: 0.7516 (tpt90) REVERT: A 1016 LYS cc_start: 0.8287 (pptt) cc_final: 0.8076 (ptmt) outliers start: 20 outliers final: 18 residues processed: 134 average time/residue: 0.1044 time to fit residues: 19.9947 Evaluate side-chains 139 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain A residue 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.6980 chunk 81 optimal weight: 0.0070 chunk 110 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 0.0000 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.0020 overall best weight: 0.2610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.192794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.153413 restraints weight = 14950.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159812 restraints weight = 7988.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.163962 restraints weight = 5388.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.166722 restraints weight = 4193.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.168368 restraints weight = 3536.132| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10903 Z= 0.100 Angle : 0.603 14.260 15045 Z= 0.291 Chirality : 0.041 0.324 1701 Planarity : 0.004 0.065 1726 Dihedral : 15.218 178.165 1996 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.00 % Allowed : 25.00 % Favored : 73.00 % 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: -1.18 (0.24), residues: 1217 helix: 0.37 (0.31), residues: 291 sheet: -0.59 (0.42), residues: 167 loop : -1.34 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 737 TYR 0.019 0.001 TYR A 199 PHE 0.019 0.001 PHE A 824 TRP 0.038 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10889) covalent geometry : angle 0.60003 / 0.29 (15036) hydrogen bonds : bond 0.02767 / 1.68 ( 278) hydrogen bonds : angle 4.72127 / 2.69 ( 796) metal coordination : bond 0.00259 / 0.17 ( 14) metal coordination : angle 2.37502 / 0.79 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.34 seconds wall clock time: 33 minutes 23.38 seconds (2003.38 seconds total)