Starting phenix.real_space_refine on Tue May 13 18:47:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x7r_33046/05_2025/7x7r_33046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7r_33046/05_2025/7x7r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x7r_33046/05_2025/7x7r_33046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7r_33046/05_2025/7x7r_33046.map" model { file = "/net/cci-nas-00/data/ceres_data/7x7r_33046/05_2025/7x7r_33046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7r_33046/05_2025/7x7r_33046.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10529 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 758 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "J" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 436 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "A" Number of atoms: 9331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1237, 9331 Classifications: {'peptide': 1237} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 59, 'TRANS': 1177} Chain breaks: 9 Unresolved non-hydrogen bonds: 662 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 535 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 25, 'TYR:plan': 1, 'ASN:plan1': 19, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 42, 'ARG:plan': 9} 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: 6.40, per 1000 atoms: 0.61 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: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.55 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: 3.83 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2879 1.33 - 1.45: 2252 1.45 - 1.57: 5606 1.57 - 1.69: 110 1.69 - 1.81: 42 Bond restraints: 10889 Sorted by residual: bond pdb=" N1 C J 23 " pdb=" C2 C J 23 " ideal model delta sigma weight residual 1.397 1.419 -0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C3' A J 19 " pdb=" O3' A J 19 " ideal model delta sigma weight residual 1.427 1.443 -0.016 1.50e-02 4.44e+03 1.19e+00 bond pdb=" N PHE A 24 " pdb=" CA PHE A 24 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.88e-01 bond pdb=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 1.607 1.618 -0.011 1.50e-02 4.44e+03 5.51e-01 bond pdb=" N ASP A 400 " pdb=" CA ASP A 400 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.54e-02 4.22e+03 5.40e-01 ... (remaining 10884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14689 1.66 - 3.33: 277 3.33 - 4.99: 54 4.99 - 6.65: 11 6.65 - 8.32: 5 Bond angle restraints: 15036 Sorted by residual: angle pdb=" C3' A J 19 " pdb=" O3' A J 19 " pdb=" P G J 20 " ideal model delta sigma weight residual 120.20 125.16 -4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" N VAL A1618 " pdb=" CA VAL A1618 " pdb=" C VAL A1618 " ideal model delta sigma weight residual 112.29 109.52 2.77 9.40e-01 1.13e+00 8.68e+00 angle pdb=" C1' C J 23 " pdb=" N1 C J 23 " pdb=" C2 C J 23 " ideal model delta sigma weight residual 118.80 127.12 -8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" C PHE A 780 " pdb=" N GLU A 781 " pdb=" CA GLU A 781 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.63e+00 angle pdb=" C PHE A 24 " pdb=" CA PHE A 24 " pdb=" CB PHE A 24 " ideal model delta sigma weight residual 110.42 115.78 -5.36 1.99e+00 2.53e-01 7.26e+00 ... (remaining 15031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 6210 35.18 - 70.36: 249 70.36 - 105.53: 32 105.53 - 140.71: 0 140.71 - 175.89: 5 Dihedral angle restraints: 6496 sinusoidal: 2968 harmonic: 3528 Sorted by residual: dihedral pdb=" O4' U C -14 " pdb=" C1' U C -14 " pdb=" N1 U C -14 " pdb=" C2 U C -14 " ideal model delta sinusoidal sigma weight residual 200.00 58.81 141.19 1 1.50e+01 4.44e-03 7.59e+01 dihedral pdb=" O4' U J 36 " pdb=" C1' U J 36 " pdb=" N1 U J 36 " pdb=" C2 U J 36 " ideal model delta sinusoidal sigma weight residual 232.00 56.11 175.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual -128.00 47.38 -175.38 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 6493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1363 0.046 - 0.091: 262 0.091 - 0.137: 70 0.137 - 0.182: 5 0.182 - 0.228: 1 Chirality restraints: 1701 Sorted by residual: chirality pdb=" CB ILE A1468 " pdb=" CA ILE A1468 " pdb=" CG1 ILE A1468 " pdb=" CG2 ILE A1468 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' A J 19 " pdb=" C4' A J 19 " pdb=" O3' A J 19 " pdb=" C2' A J 19 " both_signs ideal model delta sigma weight residual False -2.74 -2.58 -0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" C1' U C -14 " pdb=" O4' U C -14 " pdb=" C2' U C -14 " pdb=" N1 U C -14 " both_signs ideal model delta sigma weight residual False 2.47 2.31 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1698 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1475 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A1476 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1476 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1476 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 316 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 317 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 1 " 0.017 2.00e-02 2.50e+03 9.94e-03 2.22e+00 pdb=" N1 C C 1 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C C 1 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C C 1 " -0.001 2.00e-02 2.50e+03 pdb=" N3 C C 1 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C C 1 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C C 1 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C C 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C C 1 " -0.001 2.00e-02 2.50e+03 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 154 2.63 - 3.19: 9366 3.19 - 3.76: 16766 3.76 - 4.33: 22090 4.33 - 4.90: 35754 Nonbonded interactions: 84130 Sorted by model distance: nonbonded pdb=" O2' U C 5 " pdb=" O ALA A 685 " model vdw 2.058 3.040 nonbonded pdb=" O LEU A1648 " pdb=" OG1 THR A1662 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 680 " pdb=" O GLY A 859 " model vdw 2.263 3.040 nonbonded pdb=" O2' G J 20 " pdb=" O4' U J 21 " model vdw 2.263 3.040 nonbonded pdb=" NH2 ARG A 737 " pdb=" OE1 GLU A1525 " model vdw 2.264 3.120 ... (remaining 84125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.870 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10903 Z= 0.100 Angle : 0.587 8.316 15045 Z= 0.291 Chirality : 0.040 0.228 1701 Planarity : 0.003 0.043 1726 Dihedral : 18.553 175.890 4236 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.015 0.001 TRP A 862 HIS 0.004 0.001 HIS A 33 PHE 0.023 0.001 PHE A 546 TYR 0.018 0.001 TYR A 649 ARG 0.005 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.19878 ( 278) hydrogen bonds : angle 8.62184 ( 796) metal coordination : bond 0.00317 ( 14) metal coordination : angle 2.35710 ( 9) covalent geometry : bond 0.00206 (10889) covalent geometry : angle 0.58426 (15036) *********************** 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 : 1.025 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: 0.7138 (p0) REVERT: A 1004 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7184 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2441 time to fit residues: 55.2257 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 : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.3980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.191908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151915 restraints weight = 14811.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.158467 restraints weight = 7785.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162778 restraints weight = 5225.447| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.1165 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= 0.122 Angle : 0.585 8.244 15045 Z= 0.293 Chirality : 0.042 0.304 1701 Planarity : 0.004 0.043 1726 Dihedral : 19.387 176.105 2200 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.44 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.24), residues: 1217 helix: -0.00 (0.30), residues: 314 sheet: -1.03 (0.40), residues: 178 loop : -1.31 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.004 0.001 HIS A 924 PHE 0.019 0.001 PHE A 824 TYR 0.020 0.001 TYR A 199 ARG 0.005 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 278) hydrogen bonds : angle 6.06101 ( 796) metal coordination : bond 0.00506 ( 14) metal coordination : angle 3.47613 ( 9) covalent geometry : bond 0.00269 (10889) covalent geometry : angle 0.57881 (15036) *********************** 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: 13 poor density : 136 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 507 ILE cc_start: 0.7807 (mt) cc_final: 0.7195 (pt) REVERT: A 526 GLU cc_start: 0.7496 (pt0) cc_final: 0.7080 (pt0) REVERT: A 624 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7810 (tt0) REVERT: A 760 ASN cc_start: 0.7773 (p0) cc_final: 0.7307 (p0) REVERT: A 1004 ARG cc_start: 0.7734 (tpt170) cc_final: 0.7267 (tpp-160) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.2448 time to fit residues: 49.2531 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 : 1.179 ------------------------------------------------------------------------------- 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 815 LYS Chi-restraints excluded: chain A residue 924 HIS Chi-restraints excluded: chain A residue 937 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.184860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.144566 restraints weight = 15348.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.150400 restraints weight = 8602.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.154191 restraints weight = 6010.107| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10903 Z= 0.200 Angle : 0.630 10.929 15045 Z= 0.318 Chirality : 0.044 0.301 1701 Planarity : 0.005 0.068 1726 Dihedral : 19.575 177.759 2200 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 1.78 % Allowed : 15.67 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.24), residues: 1217 helix: 0.01 (0.30), residues: 308 sheet: -0.85 (0.41), residues: 178 loop : -1.44 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1530 HIS 0.008 0.001 HIS A 924 PHE 0.026 0.002 PHE A 824 TYR 0.019 0.002 TYR A 199 ARG 0.005 0.001 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 278) hydrogen bonds : angle 5.74345 ( 796) metal coordination : bond 0.00797 ( 14) metal coordination : angle 3.99842 ( 9) covalent geometry : bond 0.00455 (10889) covalent geometry : angle 0.62298 (15036) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8313 (mpp) cc_final: 0.8098 (mpp) REVERT: A 624 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7986 (tt0) REVERT: A 627 MET cc_start: 0.7990 (mtt) cc_final: 0.7729 (mtt) REVERT: A 1004 ARG cc_start: 0.7988 (tpt170) cc_final: 0.7771 (tpt90) REVERT: A 1016 LYS cc_start: 0.8182 (pptt) cc_final: 0.7859 (ptmt) outliers start: 16 outliers final: 12 residues processed: 137 average time/residue: 0.2471 time to fit residues: 48.0068 Evaluate side-chains 129 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU 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 403 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 961 LEU 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 27 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 0.0570 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 0.0770 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS A 924 HIS A1544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.187547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.146938 restraints weight = 14965.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153207 restraints weight = 8088.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.157284 restraints weight = 5511.892| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.1872 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= 0.125 Angle : 0.577 12.111 15045 Z= 0.288 Chirality : 0.042 0.300 1701 Planarity : 0.004 0.056 1726 Dihedral : 19.460 177.427 2200 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.11 % Allowed : 18.67 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1217 helix: 0.11 (0.30), residues: 302 sheet: -0.86 (0.41), residues: 176 loop : -1.34 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1530 HIS 0.004 0.001 HIS A 455 PHE 0.030 0.001 PHE A 226 TYR 0.016 0.001 TYR A 199 ARG 0.003 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 278) hydrogen bonds : angle 5.38044 ( 796) metal coordination : bond 0.00397 ( 14) metal coordination : angle 3.21440 ( 9) covalent geometry : bond 0.00278 (10889) covalent geometry : angle 0.57207 (15036) *********************** 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 167 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.184 Fit side-chains REVERT: A 36 MET cc_start: 0.8338 (mpp) cc_final: 0.8087 (mpp) REVERT: A 514 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6274 (pp) REVERT: A 563 TYR cc_start: 0.7198 (t80) cc_final: 0.6752 (t80) REVERT: A 624 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7907 (tt0) REVERT: A 627 MET cc_start: 0.7899 (mtt) cc_final: 0.7649 (mtt) REVERT: A 860 TYR cc_start: 0.8191 (m-80) cc_final: 0.7975 (m-80) REVERT: A 1004 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7551 (tpt90) REVERT: A 1016 LYS cc_start: 0.8346 (pptt) cc_final: 0.8047 (ptmt) REVERT: A 1418 HIS cc_start: 0.5835 (m-70) cc_final: 0.5463 (m-70) REVERT: A 1419 LEU cc_start: 0.6786 (tt) cc_final: 0.6571 (tt) outliers start: 28 outliers final: 14 residues processed: 156 average time/residue: 0.2341 time to fit residues: 51.6309 Evaluate side-chains 135 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU 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 507 ILE Chi-restraints excluded: chain A residue 514 LEU 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 965 ILE Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 117 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.189824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.149418 restraints weight = 14936.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.155808 restraints weight = 8002.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.159942 restraints weight = 5445.714| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10903 Z= 0.106 Angle : 0.580 13.202 15045 Z= 0.286 Chirality : 0.042 0.335 1701 Planarity : 0.004 0.073 1726 Dihedral : 19.352 177.445 2200 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.00 % Allowed : 20.00 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1217 helix: 0.17 (0.30), residues: 302 sheet: -0.69 (0.42), residues: 169 loop : -1.38 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1530 HIS 0.004 0.001 HIS A 924 PHE 0.018 0.001 PHE A 824 TYR 0.016 0.001 TYR A 199 ARG 0.004 0.000 ARG A 564 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 278) hydrogen bonds : angle 5.16722 ( 796) metal coordination : bond 0.00295 ( 14) metal coordination : angle 2.72257 ( 9) covalent geometry : bond 0.00230 (10889) covalent geometry : angle 0.57604 (15036) *********************** 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 160 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.155 Fit side-chains REVERT: A 36 MET cc_start: 0.8328 (mpp) cc_final: 0.8050 (mpp) REVERT: A 514 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6310 (pp) REVERT: A 563 TYR cc_start: 0.7152 (t80) cc_final: 0.6781 (t80) REVERT: A 624 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7894 (tt0) REVERT: A 627 MET cc_start: 0.7954 (mtt) cc_final: 0.7655 (mtt) REVERT: A 719 ARG cc_start: 0.7400 (mpt180) cc_final: 0.7163 (mpt180) REVERT: A 776 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6048 (p0) REVERT: A 1004 ARG cc_start: 0.7786 (tpt170) cc_final: 0.7432 (tpt90) REVERT: A 1016 LYS cc_start: 0.8387 (pptt) cc_final: 0.7149 (tptt) REVERT: A 1418 HIS cc_start: 0.5834 (m-70) cc_final: 0.5552 (m-70) REVERT: A 1525 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6457 (pt0) outliers start: 27 outliers final: 17 residues processed: 149 average time/residue: 0.2484 time to fit residues: 52.0790 Evaluate side-chains 139 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 547 ASP 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 796 THR Chi-restraints excluded: chain A residue 842 LEU 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 1399 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1617 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6478 > 50: distance: 5 - 9: 12.157 distance: 9 - 10: 15.308 distance: 10 - 11: 12.114 distance: 10 - 13: 31.134 distance: 11 - 12: 34.167 distance: 11 - 18: 26.543 distance: 13 - 14: 31.658 distance: 14 - 15: 27.889 distance: 15 - 16: 19.654 distance: 15 - 17: 15.501 distance: 18 - 19: 11.852 distance: 18 - 180: 11.268 distance: 19 - 20: 5.306 distance: 19 - 22: 6.546 distance: 20 - 21: 6.128 distance: 20 - 25: 5.607 distance: 21 - 177: 8.919 distance: 22 - 23: 5.424 distance: 22 - 24: 4.381 distance: 25 - 26: 6.090 distance: 26 - 27: 5.072 distance: 27 - 28: 10.359 distance: 27 - 34: 9.752 distance: 29 - 30: 8.462 distance: 30 - 31: 5.069 distance: 31 - 33: 3.304 distance: 34 - 35: 15.695 distance: 34 - 165: 9.572 distance: 35 - 36: 4.864 distance: 35 - 38: 10.716 distance: 36 - 37: 13.336 distance: 36 - 46: 9.880 distance: 37 - 162: 22.128 distance: 38 - 39: 5.447 distance: 39 - 40: 3.912 distance: 39 - 41: 6.700 distance: 40 - 42: 11.395 distance: 41 - 43: 13.370 distance: 42 - 44: 3.947 distance: 43 - 44: 3.052 distance: 46 - 47: 6.478 distance: 46 - 246: 6.515 distance: 47 - 48: 22.018 distance: 47 - 50: 7.581 distance: 48 - 49: 28.214 distance: 48 - 53: 37.098 distance: 49 - 243: 26.874 distance: 50 - 51: 13.393 distance: 50 - 52: 18.905 distance: 53 - 54: 20.830 distance: 53 - 149: 17.051 distance: 54 - 55: 21.350 distance: 54 - 57: 6.465 distance: 55 - 56: 23.226 distance: 55 - 61: 27.347 distance: 56 - 146: 25.944 distance: 57 - 58: 18.378 distance: 57 - 59: 6.874 distance: 58 - 60: 14.894 distance: 61 - 62: 23.170 distance: 62 - 63: 5.319 distance: 62 - 65: 10.651 distance: 63 - 64: 9.074 distance: 63 - 70: 11.968 distance: 65 - 66: 6.765 distance: 66 - 67: 8.565 distance: 67 - 68: 5.577 distance: 70 - 71: 28.088 distance: 70 - 133: 14.084 distance: 71 - 72: 17.545 distance: 71 - 74: 17.490 distance: 72 - 73: 31.298 distance: 72 - 77: 30.718 distance: 73 - 130: 25.223 distance: 74 - 75: 20.719 distance: 74 - 76: 26.018 distance: 77 - 78: 19.055 distance: 78 - 79: 11.790 distance: 79 - 80: 47.535 distance: 79 - 81: 38.831 distance: 81 - 82: 24.348 distance: 82 - 83: 43.077 distance: 82 - 85: 27.169 distance: 83 - 84: 37.579 distance: 83 - 87: 15.904 distance: 85 - 86: 22.763