Starting phenix.real_space_refine on Fri Sep 11 18:17:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7r_33046/09_2026/7x7r_33046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7r_33046/09_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_33046/09_2026/7x7r_33046.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x7r_33046/09_2026/7x7r_33046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x7r_33046/09_2026/7x7r_33046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7r_33046/09_2026/7x7r_33046.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7r_33046/09_2026/7x7r_33046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7r_33046/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 2.22, per 1000 atoms: 0.21 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: 0.85 Conformation dependent library (CDL) restraints added in 449.5 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: 0.87 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: 1.64 Time building geometry restraints manager: 1.15 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=" C3' A J 19 " pdb=" O3' A J 19 " ideal model delta sigma weight residual 1.415 1.443 -0.028 2.00e-02 2.50e+03 2.01e+00 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=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 1.607 1.618 -0.011 1.20e-02 6.94e+03 8.61e-01 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 C 3 " pdb=" P A C 4 " ideal model delta sigma weight residual 1.607 1.616 -0.009 1.20e-02 6.94e+03 5.45e-01 ... (remaining 10884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14442 1.66 - 3.33: 443 3.33 - 4.99: 132 4.99 - 6.65: 14 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 119.70 125.16 -5.46 1.20e+00 6.94e-01 2.07e+01 angle pdb=" C3' A C 3 " pdb=" O3' A C 3 " pdb=" P A C 4 " ideal model delta sigma weight residual 119.70 123.85 -4.15 1.20e+00 6.94e-01 1.19e+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 ... (remaining 15031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 5946 32.42 - 64.84: 309 64.84 - 97.26: 36 97.26 - 129.68: 0 129.68 - 162.09: 1 Dihedral angle restraints: 6292 sinusoidal: 2764 harmonic: 3528 Sorted by residual: dihedral pdb=" C4' U J 36 " pdb=" C3' U J 36 " pdb=" C2' U J 36 " pdb=" C1' U J 36 " ideal model delta sinusoidal sigma weight residual 36.34 -36.68 73.02 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' G J 26 " pdb=" C3' G J 26 " pdb=" C2' G J 26 " pdb=" C1' G J 26 " ideal model delta sinusoidal sigma weight residual 36.34 -36.34 72.68 1 3.10e+00 1.04e-01 7.02e+02 dihedral pdb=" C4' A C -13 " pdb=" C3' A C -13 " pdb=" C2' A C -13 " pdb=" C1' A C -13 " ideal model delta sinusoidal sigma weight residual 36.34 -36.13 72.47 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 6289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1462 0.075 - 0.149: 131 0.149 - 0.224: 7 0.224 - 0.299: 99 0.299 - 0.374: 2 Chirality restraints: 1701 Sorted by residual: chirality pdb=" P G J 20 " pdb=" OP1 G J 20 " pdb=" OP2 G J 20 " pdb=" O5' G J 20 " both_signs ideal model delta sigma weight residual True 2.17 -2.55 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" P A C 4 " pdb=" OP1 A C 4 " pdb=" OP2 A C 4 " pdb=" O5' A C 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' U J 36 " pdb=" C3' U J 36 " pdb=" O2' U J 36 " pdb=" C1' U J 36 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.550 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- 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= 0.115 Angle : 0.725 8.316 15045 Z= 0.335 Chirality : 0.074 0.374 1701 Planarity : 0.003 0.043 1726 Dihedral : 18.576 162.094 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 0.00236 / 0.11 (10889) covalent geometry : angle 0.72341 / 0.34 (15036) hydrogen bonds : bond 0.19878 / 10.60 ( 278) hydrogen bonds : angle 8.62184 / 3.25 ( 796) metal coordination : bond 0.00317 / 0.16 ( 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 : 0.429 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: 0.0987 time to fit residues: 22.8762 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 : 0.333 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.193945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.153908 restraints weight = 15119.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160420 restraints weight = 7974.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164820 restraints weight = 5369.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.167688 restraints weight = 4150.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.169406 restraints weight = 3492.735| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10903 Z= 0.183 Angle : 1.086 19.834 15045 Z= 0.451 Chirality : 0.108 1.729 1701 Planarity : 0.005 0.044 1726 Dihedral : 16.044 170.091 1996 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.33 % Allowed : 10.11 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.24), residues: 1217 helix: 0.03 (0.30), residues: 314 sheet: -0.99 (0.43), residues: 159 loop : -1.37 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 180 TYR 0.021 0.002 TYR A 199 PHE 0.018 0.001 PHE A 824 TRP 0.008 0.001 TRP A1442 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (10889) covalent geometry : angle 1.08322 / 0.45 (15036) hydrogen bonds : bond 0.04442 / 2.44 ( 278) hydrogen bonds : angle 6.13367 / 2.28 ( 796) metal coordination : bond 0.00510 / 0.26 ( 14) metal coordination : angle 3.52820 / 1.18 ( 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 : 0.364 Fit side-chains revert: symmetry clash REVERT: A 507 ILE cc_start: 0.7856 (mt) cc_final: 0.7242 (pt) REVERT: A 526 GLU cc_start: 0.7466 (pt0) cc_final: 0.7052 (pt0) REVERT: A 624 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7824 (tt0) REVERT: A 760 ASN cc_start: 0.7802 (p0) cc_final: 0.7327 (p0) outliers start: 12 outliers final: 7 residues processed: 142 average time/residue: 0.0932 time to fit residues: 18.9440 Evaluate side-chains 123 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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: 0.2980 chunk 126 optimal weight: 0.0040 chunk 91 optimal weight: 7.9990 chunk 122 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.4774 ------------------------------------------------------------------------------- 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 = 0.4417 r_free = 0.4417 target = 0.189676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150239 restraints weight = 14732.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.156267 restraints weight = 8129.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.160284 restraints weight = 5569.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.162919 restraints weight = 4345.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.164637 restraints weight = 3690.141| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10903 Z= 0.207 Angle : 0.910 18.479 15045 Z= 0.399 Chirality : 0.080 0.768 1701 Planarity : 0.005 0.085 1726 Dihedral : 16.337 176.088 1996 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.44 % Allowed : 15.56 % Favored : 82.00 % 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: -1.43 (0.25), residues: 1217 helix: 0.05 (0.30), residues: 293 sheet: -0.95 (0.41), residues: 178 loop : -1.40 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.019 0.002 TYR A 199 PHE 0.026 0.002 PHE A 824 TRP 0.017 0.001 TRP A1530 HIS 0.014 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (10889) covalent geometry : angle 0.90465 / 0.40 (15036) hydrogen bonds : bond 0.03871 / 2.02 ( 278) hydrogen bonds : angle 5.76516 / 2.15 ( 796) metal coordination : bond 0.00768 / 0.38 ( 14) metal coordination : angle 4.05988 / 1.35 ( 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 151 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8168 (mpp) cc_final: 0.7953 (mpp) REVERT: A 526 GLU cc_start: 0.7576 (pt0) cc_final: 0.7107 (pt0) REVERT: A 624 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7996 (tt0) REVERT: A 627 MET cc_start: 0.7978 (mtt) cc_final: 0.7711 (mtt) REVERT: A 1002 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: A 1016 LYS cc_start: 0.8113 (pptt) cc_final: 0.7804 (ptmt) outliers start: 22 outliers final: 12 residues processed: 141 average time/residue: 0.0985 time to fit residues: 19.6763 Evaluate side-chains 128 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR 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 606 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1467 SER 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: 1.9990 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147874 restraints weight = 15396.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.153458 restraints weight = 8940.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.157058 restraints weight = 6348.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.159434 restraints weight = 5103.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.160762 restraints weight = 4419.195| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10903 Z= 0.224 Angle : 0.895 18.375 15045 Z= 0.396 Chirality : 0.076 0.735 1701 Planarity : 0.005 0.062 1726 Dihedral : 16.459 179.660 1996 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.78 % Allowed : 18.56 % Favored : 77.67 % 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: -1.60 (0.24), residues: 1217 helix: -0.09 (0.30), residues: 289 sheet: -0.91 (0.42), residues: 173 loop : -1.54 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 476 TYR 0.018 0.002 TYR A 199 PHE 0.033 0.002 PHE A 226 TRP 0.017 0.002 TRP A1530 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (10889) covalent geometry : angle 0.89031 / 0.40 (15036) hydrogen bonds : bond 0.03719 / 1.94 ( 278) hydrogen bonds : angle 5.69505 / 2.12 ( 796) metal coordination : bond 0.00745 / 0.37 ( 14) metal coordination : angle 4.02274 / 1.34 ( 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 162 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.314 Fit side-chains REVERT: A 36 MET cc_start: 0.8223 (mpp) cc_final: 0.7979 (mpp) REVERT: A 624 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7947 (tt0) REVERT: A 627 MET cc_start: 0.8039 (mtt) cc_final: 0.7759 (mtt) REVERT: A 1002 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: A 1016 LYS cc_start: 0.8136 (pptt) cc_final: 0.7867 (ptmt) outliers start: 34 outliers final: 18 residues processed: 148 average time/residue: 0.0955 time to fit residues: 20.3886 Evaluate side-chains 135 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1006 MET Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 455 HIS A 466 ASN A 924 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.191396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152237 restraints weight = 15070.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.158495 restraints weight = 8169.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.162633 restraints weight = 5531.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.165156 restraints weight = 4289.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.167051 restraints weight = 3652.998| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2693 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= 0.142 Angle : 0.810 15.964 15045 Z= 0.356 Chirality : 0.068 0.647 1701 Planarity : 0.004 0.054 1726 Dihedral : 16.358 178.785 1996 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.89 % Allowed : 20.67 % Favored : 76.44 % 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: -1.49 (0.25), residues: 1217 helix: 0.06 (0.30), residues: 289 sheet: -1.02 (0.41), residues: 178 loop : -1.44 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.018 0.002 TYR A 199 PHE 0.020 0.001 PHE A 824 TRP 0.021 0.001 TRP A1530 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10889) covalent geometry : angle 0.80646 / 0.36 (15036) hydrogen bonds : bond 0.03160 / 1.65 ( 278) hydrogen bonds : angle 5.32360 / 1.98 ( 796) metal coordination : bond 0.00374 / 0.19 ( 14) metal coordination : angle 3.13015 / 1.04 ( 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 158 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8174 (mpp) cc_final: 0.7876 (mpp) REVERT: A 167 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5220 (pp) REVERT: A 526 GLU cc_start: 0.7476 (pt0) cc_final: 0.7149 (pt0) REVERT: A 624 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7900 (tt0) REVERT: A 627 MET cc_start: 0.7992 (mtt) cc_final: 0.7646 (mtt) REVERT: A 1002 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: A 1016 LYS cc_start: 0.8338 (pptt) cc_final: 0.8089 (ptmt) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 0.0970 time to fit residues: 20.4157 Evaluate side-chains 140 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU 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 514 LEU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 949 LEU 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 1002 GLU Chi-restraints excluded: chain A residue 1399 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 21 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 466 ASN A 776 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.191988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152953 restraints weight = 14558.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.159357 restraints weight = 7779.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.163539 restraints weight = 5190.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.166329 restraints weight = 3993.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167945 restraints weight = 3347.090| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10903 Z= 0.141 Angle : 0.803 15.463 15045 Z= 0.353 Chirality : 0.066 0.618 1701 Planarity : 0.004 0.075 1726 Dihedral : 16.301 179.978 1996 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.45 % Rotamer: Outliers : 3.89 % Allowed : 21.78 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.24), residues: 1217 helix: 0.09 (0.30), residues: 289 sheet: -1.03 (0.41), residues: 178 loop : -1.44 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.023 0.002 TYR A 621 PHE 0.022 0.001 PHE A 824 TRP 0.023 0.001 TRP A1530 HIS 0.010 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10889) covalent geometry : angle 0.79954 / 0.35 (15036) hydrogen bonds : bond 0.03136 / 1.65 ( 278) hydrogen bonds : angle 5.19894 / 1.93 ( 796) metal coordination : bond 0.00339 / 0.17 ( 14) metal coordination : angle 3.02233 / 1.01 ( 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 157 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8217 (mpp) cc_final: 0.7878 (mpp) REVERT: A 51 ARG cc_start: 0.6668 (ttm110) cc_final: 0.6447 (mtp85) REVERT: A 167 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5230 (pp) REVERT: A 624 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7887 (tt0) REVERT: A 627 MET cc_start: 0.8023 (mtt) cc_final: 0.7612 (mtt) REVERT: A 1002 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7249 (tp30) REVERT: A 1016 LYS cc_start: 0.8335 (pptt) cc_final: 0.7239 (tptt) REVERT: A 1512 MET cc_start: 0.7021 (mmm) cc_final: 0.6583 (mmm) REVERT: A 1525 GLU cc_start: 0.6774 (mt-10) cc_final: 0.6550 (pt0) outliers start: 35 outliers final: 23 residues processed: 145 average time/residue: 0.0964 time to fit residues: 19.7543 Evaluate side-chains 142 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 937 LYS Chi-restraints excluded: chain A residue 949 LEU 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 1002 GLU 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: 2.9990 chunk 127 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 80 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 466 ASN A 924 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.194283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155882 restraints weight = 14469.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162165 restraints weight = 7857.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.166241 restraints weight = 5301.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.168947 restraints weight = 4110.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.170518 restraints weight = 3461.442| |-----------------------------------------------------------------------------| r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10903 Z= 0.124 Angle : 0.773 14.109 15045 Z= 0.340 Chirality : 0.063 0.535 1701 Planarity : 0.004 0.051 1726 Dihedral : 16.164 177.699 1996 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.33 % Allowed : 23.78 % Favored : 72.89 % 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: -1.39 (0.25), residues: 1217 helix: 0.18 (0.30), residues: 289 sheet: -0.91 (0.41), residues: 173 loop : -1.42 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 51 TYR 0.020 0.002 TYR A 621 PHE 0.019 0.001 PHE A 824 TRP 0.027 0.001 TRP A1530 HIS 0.007 0.001 HIS A1418 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10889) covalent geometry : angle 0.77065 / 0.34 (15036) hydrogen bonds : bond 0.02940 / 1.55 ( 278) hydrogen bonds : angle 5.00899 / 1.86 ( 796) metal coordination : bond 0.00280 / 0.14 ( 14) metal coordination : angle 2.58931 / 0.86 ( 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 154 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8139 (mpp) cc_final: 0.7812 (mpp) REVERT: A 167 LEU cc_start: 0.5652 (OUTLIER) cc_final: 0.5239 (pp) REVERT: A 624 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8026 (tt0) REVERT: A 627 MET cc_start: 0.8120 (mtt) cc_final: 0.7648 (mtt) REVERT: A 1002 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: A 1016 LYS cc_start: 0.8170 (pptt) cc_final: 0.7157 (tptt) REVERT: A 1512 MET cc_start: 0.7193 (mmm) cc_final: 0.6881 (mmm) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.1033 time to fit residues: 20.9373 Evaluate side-chains 136 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 924 HIS 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 1002 GLU Chi-restraints excluded: chain A residue 1006 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 HIS A 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.185059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145020 restraints weight = 15090.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.151039 restraints weight = 8343.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.154897 restraints weight = 5715.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157517 restraints weight = 4503.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.159102 restraints weight = 3842.472| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10903 Z= 0.215 Angle : 0.860 15.324 15045 Z= 0.382 Chirality : 0.068 0.580 1701 Planarity : 0.005 0.069 1726 Dihedral : 16.210 175.061 1996 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.19 % Favored : 89.73 % Rotamer: Outliers : 3.67 % Allowed : 24.56 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.24), residues: 1217 helix: -0.04 (0.30), residues: 290 sheet: -1.02 (0.41), residues: 177 loop : -1.49 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 476 TYR 0.036 0.002 TYR A 925 PHE 0.030 0.002 PHE A 824 TRP 0.028 0.002 TRP A1530 HIS 0.009 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (10889) covalent geometry : angle 0.85333 / 0.38 (15036) hydrogen bonds : bond 0.03536 / 1.87 ( 278) hydrogen bonds : angle 5.28083 / 1.97 ( 796) metal coordination : bond 0.00633 / 0.32 ( 14) metal coordination : angle 4.41838 / 1.47 ( 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 154 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8288 (mpp) cc_final: 0.7914 (mpp) REVERT: A 133 LEU cc_start: 0.8734 (mt) cc_final: 0.8447 (mm) REVERT: A 167 LEU cc_start: 0.5754 (OUTLIER) cc_final: 0.5355 (pp) REVERT: A 168 ARG cc_start: 0.7053 (tpm170) cc_final: 0.6693 (tpm170) REVERT: A 624 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7888 (tt0) REVERT: A 627 MET cc_start: 0.8054 (mtt) cc_final: 0.7644 (mtt) REVERT: A 1002 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7151 (mm-30) REVERT: A 1016 LYS cc_start: 0.8371 (pptt) cc_final: 0.7282 (tptt) REVERT: A 1512 MET cc_start: 0.7133 (mmm) cc_final: 0.6874 (mmm) REVERT: A 1525 GLU cc_start: 0.7034 (pt0) cc_final: 0.6543 (pt0) outliers start: 33 outliers final: 25 residues processed: 140 average time/residue: 0.0969 time to fit residues: 19.1666 Evaluate side-chains 148 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LEU 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 807 THR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 863 VAL 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 1002 GLU Chi-restraints excluded: chain A residue 1006 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 924 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.191174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.152227 restraints weight = 14995.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.158366 restraints weight = 8227.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162378 restraints weight = 5601.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.165036 restraints weight = 4371.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.166796 restraints weight = 3708.371| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3072 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= 0.139 Angle : 0.798 14.316 15045 Z= 0.351 Chirality : 0.064 0.551 1701 Planarity : 0.004 0.054 1726 Dihedral : 16.191 174.609 1996 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.33 % Allowed : 25.00 % Favored : 71.67 % 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: -1.48 (0.25), residues: 1217 helix: 0.08 (0.30), residues: 296 sheet: -1.04 (0.40), residues: 182 loop : -1.45 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 476 TYR 0.019 0.002 TYR A 199 PHE 0.022 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 0.00315 / 0.14 (10889) covalent geometry : angle 0.79464 / 0.35 (15036) hydrogen bonds : bond 0.03088 / 1.63 ( 278) hydrogen bonds : angle 5.06981 / 1.90 ( 796) metal coordination : bond 0.00422 / 0.21 ( 14) metal coordination : angle 3.07343 / 1.02 ( 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 157 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8243 (mpp) cc_final: 0.7879 (mpp) REVERT: A 133 LEU cc_start: 0.8670 (mt) cc_final: 0.8326 (mm) REVERT: A 167 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5370 (pp) REVERT: A 168 ARG cc_start: 0.6969 (tpm170) cc_final: 0.6538 (tpm170) REVERT: A 624 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7984 (tt0) REVERT: A 627 MET cc_start: 0.8121 (mtt) cc_final: 0.7663 (mtt) REVERT: A 922 TYR cc_start: 0.6432 (t80) cc_final: 0.5639 (t80) REVERT: A 1002 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: A 1016 LYS cc_start: 0.8292 (pptt) cc_final: 0.8083 (ptmt) REVERT: A 1512 MET cc_start: 0.7116 (mmm) cc_final: 0.6911 (mmm) REVERT: A 1525 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6492 (pt0) outliers start: 30 outliers final: 21 residues processed: 144 average time/residue: 0.1022 time to fit residues: 20.9942 Evaluate side-chains 144 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 514 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 838 ILE 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 1002 GLU Chi-restraints excluded: chain A residue 1006 MET 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 1525 GLU 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: 5.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 62 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 44 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 776 ASN A 924 HIS ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.193878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.155762 restraints weight = 14570.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.161987 restraints weight = 7907.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.166103 restraints weight = 5320.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.168827 restraints weight = 4109.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.170385 restraints weight = 3451.731| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.3112 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= 0.124 Angle : 0.786 14.656 15045 Z= 0.345 Chirality : 0.062 0.496 1701 Planarity : 0.004 0.047 1726 Dihedral : 16.170 174.940 1996 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.56 % Allowed : 25.78 % Favored : 71.67 % 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: -1.42 (0.25), residues: 1217 helix: 0.13 (0.30), residues: 296 sheet: -0.80 (0.40), residues: 181 loop : -1.47 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 476 TYR 0.019 0.002 TYR A 199 PHE 0.019 0.001 PHE A 824 TRP 0.035 0.001 TRP A1530 HIS 0.012 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10889) covalent geometry : angle 0.78265 / 0.35 (15036) hydrogen bonds : bond 0.02973 / 1.57 ( 278) hydrogen bonds : angle 4.97313 / 1.86 ( 796) metal coordination : bond 0.00337 / 0.17 ( 14) metal coordination : angle 3.11705 / 1.04 ( 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 146 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8172 (mpp) cc_final: 0.7818 (mpp) REVERT: A 133 LEU cc_start: 0.8705 (mt) cc_final: 0.8343 (mm) REVERT: A 167 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5174 (pp) REVERT: A 168 ARG cc_start: 0.6914 (tpm170) cc_final: 0.6637 (tpm170) REVERT: A 624 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8049 (tt0) REVERT: A 627 MET cc_start: 0.8184 (mtt) cc_final: 0.7710 (mtt) REVERT: A 719 ARG cc_start: 0.7467 (mpt180) cc_final: 0.7252 (mpt180) REVERT: A 1002 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: A 1525 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6671 (pt0) REVERT: A 1531 GLU cc_start: 0.7230 (pt0) cc_final: 0.6751 (tt0) outliers start: 23 outliers final: 19 residues processed: 136 average time/residue: 0.1042 time to fit residues: 20.2037 Evaluate side-chains 138 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 514 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 776 ASN 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 1002 GLU 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 1525 GLU 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: 0.7980 chunk 110 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 105 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 466 ASN A 776 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.193914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.155998 restraints weight = 14533.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162114 restraints weight = 8012.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.166190 restraints weight = 5436.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.168919 restraints weight = 4197.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.170569 restraints weight = 3525.559| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 10903 Z= 0.248 Angle : 1.079 59.185 15045 Z= 0.596 Chirality : 0.073 1.193 1701 Planarity : 0.007 0.213 1726 Dihedral : 16.167 174.923 1996 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 2.67 % Allowed : 26.11 % Favored : 71.22 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.25), residues: 1217 helix: 0.12 (0.30), residues: 296 sheet: -0.79 (0.40), residues: 181 loop : -1.47 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 476 TYR 0.018 0.002 TYR A 199 PHE 0.020 0.001 PHE A 824 TRP 0.031 0.001 TRP A1530 HIS 0.356 0.008 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.25 (10889) covalent geometry : angle 1.07660 / 0.60 (15036) hydrogen bonds : bond 0.02976 / 1.57 ( 278) hydrogen bonds : angle 4.97236 / 1.86 ( 796) metal coordination : bond 0.00347 / 0.17 ( 14) metal coordination : angle 3.10964 / 1.04 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1719.26 seconds wall clock time: 30 minutes 30.87 seconds (1830.87 seconds total)