Starting phenix.real_space_refine on Tue Jan 21 09:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ea8_31040/01_2025/7ea8_31040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ea8_31040/01_2025/7ea8_31040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ea8_31040/01_2025/7ea8_31040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ea8_31040/01_2025/7ea8_31040.map" model { file = "/net/cci-nas-00/data/ceres_data/7ea8_31040/01_2025/7ea8_31040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ea8_31040/01_2025/7ea8_31040.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4902 atoms to isotropic. 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 3 6.06 5 P 244 5.49 5 S 33 5.16 5 C 7305 2.51 5 N 2401 2.21 5 O 2879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12865 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1993 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain: "A" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 818 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 799 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 794 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2485 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2517 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 643 SG CYS L1529 40.601 58.945 52.919 1.00 46.92 S ATOM 672 SG CYS L1533 40.198 62.627 55.544 1.00 53.00 S ATOM 717 SG CYS L1539 40.330 62.668 51.612 1.00 47.82 S ATOM 416 SG CYS L1499 43.510 60.073 56.178 1.00 47.21 S ATOM 431 SG CYS L1501 46.699 61.864 55.722 1.00 51.47 S ATOM 542 SG CYS L1516 43.708 62.969 53.053 1.00 45.67 S ATOM 569 SG CYS L1520 45.259 58.912 52.403 1.00 43.65 S ATOM 1863 SG CYS L1678 39.772 46.170 17.879 1.00 67.56 S ATOM 1909 SG CYS L1685 43.414 44.340 16.211 1.00 57.15 S Time building chain proxies: 7.97, per 1000 atoms: 0.62 Number of scatterers: 12865 At special positions: 0 Unit cell: (132, 88, 141.9, 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 3 29.99 S 33 16.00 P 244 15.00 O 2879 8.00 N 2401 7.00 C 7305 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L1801 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1539 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1533 " pdb="ZN ZN L1801 " - pdb=" SG CYS L1529 " pdb=" ZN L1802 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1520 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1499 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1516 " pdb="ZN ZN L1802 " - pdb=" SG CYS L1501 " pdb=" ZN L1803 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1678 " pdb="ZN ZN L1803 " - pdb=" SG CYS L1685 " Number of angles added : 12 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 57.7% alpha, 4.6% beta 121 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'L' and resid 1520 through 1525 removed outlier: 3.660A pdb=" N LEU L1524 " --> pdb=" O CYS L1520 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU L1525 " --> pdb=" O LEU L1521 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1520 through 1525' Processing helix chain 'L' and resid 1535 through 1539 removed outlier: 4.046A pdb=" N CYS L1539 " --> pdb=" O GLY L1536 " (cutoff:3.500A) Processing helix chain 'L' and resid 1585 through 1597 removed outlier: 4.080A pdb=" N PHE L1589 " --> pdb=" O ASP L1585 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS L1590 " --> pdb=" O HIS L1586 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L1591 " --> pdb=" O LYS L1587 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L1594 " --> pdb=" O LYS L1590 " (cutoff:3.500A) Processing helix chain 'L' and resid 1598 through 1600 No H-bonds generated for 'chain 'L' and resid 1598 through 1600' Processing helix chain 'L' and resid 1622 through 1626 removed outlier: 3.531A pdb=" N ARG L1625 " --> pdb=" O ASN L1622 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE L1626 " --> pdb=" O CYS L1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1622 through 1626' Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.597A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.657A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.849A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.748A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.738A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.996A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.706A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.815A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.659A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.905A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 122 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.792A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.044A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.718A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.026A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.978A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.912A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.718A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 83 " --> pdb=" O ARG H 79 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 1556 through 1558 removed outlier: 4.337A pdb=" N GLU L1558 " --> pdb=" O GLY L1561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 1575 through 1578 removed outlier: 6.954A pdb=" N PHE L1650 " --> pdb=" O VAL L1576 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU L1578 " --> pdb=" O VAL L1648 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL L1648 " --> pdb=" O GLU L1578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 1582 through 1583 Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.068A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.322A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.110A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.904A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.302A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 392 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 628 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2951 1.34 - 1.46: 4033 1.46 - 1.58: 6070 1.58 - 1.70: 486 1.70 - 1.82: 49 Bond restraints: 13589 Sorted by residual: bond pdb=" C2 SAM L1804 " pdb=" N3 SAM L1804 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.26e+00 bond pdb=" C8 SAM L1804 " pdb=" N7 SAM L1804 " ideal model delta sigma weight residual 1.298 1.353 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C2 SAM L1804 " pdb=" N1 SAM L1804 " ideal model delta sigma weight residual 1.329 1.381 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C6 SAM L1804 " pdb=" N1 SAM L1804 " ideal model delta sigma weight residual 1.337 1.380 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.82e+00 ... (remaining 13584 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 18677 1.70 - 3.39: 633 3.39 - 5.09: 46 5.09 - 6.79: 14 6.79 - 8.48: 5 Bond angle restraints: 19375 Sorted by residual: angle pdb=" N SER L1490 " pdb=" CA SER L1490 " pdb=" C SER L1490 " ideal model delta sigma weight residual 110.97 114.53 -3.56 1.09e+00 8.42e-01 1.07e+01 angle pdb=" N VAL D 48 " pdb=" CA VAL D 48 " pdb=" C VAL D 48 " ideal model delta sigma weight residual 113.39 108.67 4.72 1.47e+00 4.63e-01 1.03e+01 angle pdb=" C LYS L1489 " pdb=" N SER L1490 " pdb=" CA SER L1490 " ideal model delta sigma weight residual 120.65 124.65 -4.00 1.32e+00 5.74e-01 9.18e+00 angle pdb=" N1 SAM L1804 " pdb=" C2 SAM L1804 " pdb=" N3 SAM L1804 " ideal model delta sigma weight residual 128.51 120.03 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" O SAM L1804 " pdb=" C SAM L1804 " pdb=" OXT SAM L1804 " ideal model delta sigma weight residual 126.77 118.53 8.24 3.00e+00 1.11e-01 7.54e+00 ... (remaining 19370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.88: 6140 27.88 - 55.77: 1308 55.77 - 83.65: 111 83.65 - 111.53: 0 111.53 - 139.41: 3 Dihedral angle restraints: 7562 sinusoidal: 4718 harmonic: 2844 Sorted by residual: dihedral pdb=" CA TYR L1666 " pdb=" C TYR L1666 " pdb=" N GLN L1667 " pdb=" CA GLN L1667 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLU L1478 " pdb=" C GLU L1478 " pdb=" N ASN L1479 " pdb=" CA ASN L1479 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 80.59 139.41 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 7559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1775 0.052 - 0.104: 326 0.104 - 0.156: 67 0.156 - 0.208: 4 0.208 - 0.260: 1 Chirality restraints: 2173 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE L1494 " pdb=" CA ILE L1494 " pdb=" CG1 ILE L1494 " pdb=" CG2 ILE L1494 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 2170 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 103 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO C 80 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO D 103 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.028 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3109 2.82 - 3.34: 10018 3.34 - 3.86: 22773 3.86 - 4.38: 26823 4.38 - 4.90: 39763 Nonbonded interactions: 102486 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.306 3.040 nonbonded pdb=" ND2 ASN L1634 " pdb=" O GLU L1661 " model vdw 2.379 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.381 3.120 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.382 3.040 nonbonded pdb=" O GLU L1578 " pdb=" ND2 ASN L1622 " model vdw 2.387 3.120 ... (remaining 102481 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 76 or resid 78 through 133)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 123) selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13589 Z= 0.220 Angle : 0.709 8.483 19375 Z= 0.422 Chirality : 0.043 0.260 2173 Planarity : 0.006 0.051 1621 Dihedral : 24.060 139.413 5732 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -3.23 (0.21), residues: 964 helix: -1.58 (0.17), residues: 540 sheet: -2.04 (0.90), residues: 31 loop : -2.88 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L1640 HIS 0.005 0.001 HIS F 75 PHE 0.021 0.002 PHE L1664 TYR 0.024 0.002 TYR H 42 ARG 0.006 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: L 1486 LYS cc_start: 0.4525 (pmtt) cc_final: 0.4282 (mmtt) REVERT: L 1599 ASN cc_start: 0.4018 (m-40) cc_final: 0.3671 (t0) REVERT: B 68 ASP cc_start: 0.7662 (m-30) cc_final: 0.7440 (m-30) REVERT: C 75 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8335 (mmtt) REVERT: D 62 MET cc_start: 0.8493 (mmm) cc_final: 0.8250 (mmm) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.4623 time to fit residues: 135.5506 Evaluate side-chains 157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 chunk 107 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1545 GLN L1548 GLN ** L1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1667 GLN L1684 ASN A 39 HIS A 68 GLN B 93 GLN C 68 ASN D 109 HIS E 68 GLN F 27 GLN H 47 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.195965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.153473 restraints weight = 14194.641| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.26 r_work: 0.3272 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13589 Z= 0.171 Angle : 0.525 6.703 19375 Z= 0.313 Chirality : 0.034 0.140 2173 Planarity : 0.004 0.041 1621 Dihedral : 28.468 144.083 3773 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.33 % Allowed : 7.96 % Favored : 90.71 % 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: -0.89 (0.26), residues: 964 helix: 0.77 (0.22), residues: 550 sheet: -1.76 (0.88), residues: 33 loop : -2.61 (0.26), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L1562 HIS 0.003 0.001 HIS D 109 PHE 0.011 0.001 PHE L1664 TYR 0.013 0.001 TYR H 42 ARG 0.004 0.000 ARG G 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 1459 ARG cc_start: 0.5559 (ptt-90) cc_final: 0.5135 (ptm-80) REVERT: L 1514 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5943 (pp) REVERT: A 73 GLU cc_start: 0.8124 (tt0) cc_final: 0.7897 (tt0) REVERT: C 75 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8680 (mmtt) REVERT: G 36 LYS cc_start: 0.8232 (tttt) cc_final: 0.7754 (mmtm) REVERT: H 47 GLN cc_start: 0.8342 (mt0) cc_final: 0.8068 (mt0) outliers start: 11 outliers final: 5 residues processed: 175 average time/residue: 0.3848 time to fit residues: 86.8479 Evaluate side-chains 151 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1461 LYS Chi-restraints excluded: chain L residue 1514 ILE Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 116 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.150463 restraints weight = 14086.238| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.24 r_work: 0.3215 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13589 Z= 0.184 Angle : 0.521 5.516 19375 Z= 0.310 Chirality : 0.035 0.146 2173 Planarity : 0.004 0.040 1621 Dihedral : 28.494 146.781 3773 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.21 % Allowed : 8.20 % Favored : 90.59 % 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: 0.08 (0.27), residues: 964 helix: 1.76 (0.23), residues: 544 sheet: -1.50 (0.91), residues: 28 loop : -2.46 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L1562 HIS 0.004 0.001 HIS L1586 PHE 0.018 0.002 PHE L1589 TYR 0.009 0.001 TYR C 57 ARG 0.003 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.206 Fit side-chains REVERT: A 73 GLU cc_start: 0.8101 (tt0) cc_final: 0.7860 (tt0) REVERT: A 115 LYS cc_start: 0.7424 (mttp) cc_final: 0.7183 (mtmm) REVERT: B 92 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7457 (ttp80) REVERT: G 36 LYS cc_start: 0.8290 (tttt) cc_final: 0.7728 (mmtm) REVERT: H 76 GLU cc_start: 0.7968 (tp30) cc_final: 0.7754 (tp30) outliers start: 10 outliers final: 6 residues processed: 150 average time/residue: 0.3804 time to fit residues: 74.5879 Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1461 LYS Chi-restraints excluded: chain L residue 1636 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L1541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.191336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.147418 restraints weight = 13974.923| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.21 r_work: 0.3187 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13589 Z= 0.196 Angle : 0.525 5.895 19375 Z= 0.311 Chirality : 0.035 0.132 2173 Planarity : 0.004 0.039 1621 Dihedral : 28.467 147.215 3773 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.84 % Allowed : 11.22 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.47 (0.28), residues: 964 helix: 2.12 (0.23), residues: 541 sheet: -1.09 (0.96), residues: 28 loop : -2.34 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L1562 HIS 0.004 0.001 HIS D 82 PHE 0.017 0.002 PHE G 25 TYR 0.011 0.001 TYR L1596 ARG 0.004 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.948 Fit side-chains REVERT: L 1504 LEU cc_start: 0.2903 (tt) cc_final: 0.2185 (tp) REVERT: L 1606 PHE cc_start: 0.6995 (m-10) cc_final: 0.6667 (m-10) REVERT: A 42 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8080 (mmm160) REVERT: A 115 LYS cc_start: 0.7520 (mttp) cc_final: 0.7264 (mtmm) REVERT: B 92 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7548 (ttp80) REVERT: D 85 LYS cc_start: 0.8834 (mmtm) cc_final: 0.8603 (mmtm) REVERT: G 36 LYS cc_start: 0.8329 (tttt) cc_final: 0.7725 (mmtm) outliers start: 7 outliers final: 6 residues processed: 150 average time/residue: 0.3633 time to fit residues: 71.3417 Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 38 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1466 GLN L1541 ASN L1548 GLN L1549 HIS H 109 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.193211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152421 restraints weight = 14135.709| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.25 r_work: 0.3223 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13589 Z= 0.163 Angle : 0.502 5.977 19375 Z= 0.300 Chirality : 0.034 0.133 2173 Planarity : 0.003 0.037 1621 Dihedral : 28.381 148.077 3773 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.09 % Allowed : 11.46 % Favored : 87.45 % 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: 0.89 (0.28), residues: 964 helix: 2.45 (0.23), residues: 540 sheet: -1.08 (0.98), residues: 28 loop : -2.12 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L1562 HIS 0.003 0.001 HIS D 82 PHE 0.012 0.001 PHE L1589 TYR 0.008 0.001 TYR L1596 ARG 0.005 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.138 Fit side-chains REVERT: L 1504 LEU cc_start: 0.3347 (tt) cc_final: 0.2654 (tp) REVERT: L 1606 PHE cc_start: 0.6915 (m-10) cc_final: 0.6561 (m-10) REVERT: A 42 ARG cc_start: 0.8433 (mmt-90) cc_final: 0.8056 (mmm160) REVERT: A 115 LYS cc_start: 0.7331 (mttp) cc_final: 0.7095 (mtmm) REVERT: B 92 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7876 (ttp80) REVERT: C 89 ASN cc_start: 0.8647 (m-40) cc_final: 0.8384 (m-40) REVERT: D 85 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8616 (mmtm) REVERT: G 36 LYS cc_start: 0.8334 (tttt) cc_final: 0.7757 (mmtm) REVERT: H 93 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7622 (mm-30) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.3743 time to fit residues: 72.5139 Evaluate side-chains 150 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.186823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.143629 restraints weight = 14311.015| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.23 r_work: 0.3138 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13589 Z= 0.296 Angle : 0.584 6.842 19375 Z= 0.341 Chirality : 0.038 0.129 2173 Planarity : 0.004 0.042 1621 Dihedral : 28.560 147.262 3773 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.57 % Allowed : 11.46 % Favored : 86.97 % 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: 0.39 (0.28), residues: 964 helix: 1.96 (0.23), residues: 548 sheet: -1.28 (0.94), residues: 28 loop : -2.29 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L1562 HIS 0.005 0.001 HIS A 113 PHE 0.020 0.002 PHE A 84 TYR 0.012 0.002 TYR D 121 ARG 0.005 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.093 Fit side-chains REVERT: L 1582 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5621 (tp30) REVERT: L 1606 PHE cc_start: 0.6842 (m-10) cc_final: 0.6554 (m-10) REVERT: L 1638 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: A 115 LYS cc_start: 0.7871 (mttp) cc_final: 0.7515 (mtmm) REVERT: B 92 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7856 (ttp80) outliers start: 13 outliers final: 7 residues processed: 156 average time/residue: 0.3789 time to fit residues: 77.0067 Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 6 optimal weight: 0.0060 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.189563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145388 restraints weight = 14071.112| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.04 r_work: 0.3194 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13589 Z= 0.182 Angle : 0.532 8.894 19375 Z= 0.316 Chirality : 0.036 0.137 2173 Planarity : 0.004 0.040 1621 Dihedral : 28.490 148.026 3773 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.72 % Allowed : 13.03 % Favored : 86.25 % 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: 0.76 (0.28), residues: 964 helix: 2.25 (0.23), residues: 546 sheet: -1.16 (0.95), residues: 28 loop : -2.08 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L1562 HIS 0.004 0.001 HIS D 82 PHE 0.018 0.002 PHE L1575 TYR 0.011 0.001 TYR H 42 ARG 0.005 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 1.178 Fit side-chains REVERT: L 1504 LEU cc_start: 0.2869 (tt) cc_final: 0.2135 (tp) REVERT: L 1582 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5703 (tp30) REVERT: L 1606 PHE cc_start: 0.6838 (m-10) cc_final: 0.6558 (m-10) REVERT: L 1638 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7840 (mt0) REVERT: A 42 ARG cc_start: 0.8542 (mmt-90) cc_final: 0.8149 (mmm160) REVERT: A 115 LYS cc_start: 0.7613 (mttp) cc_final: 0.7288 (mtmm) REVERT: B 92 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7893 (ttp80) REVERT: G 36 LYS cc_start: 0.8337 (tttt) cc_final: 0.7754 (mmtm) outliers start: 6 outliers final: 4 residues processed: 150 average time/residue: 0.3758 time to fit residues: 73.8176 Evaluate side-chains 149 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 1638 GLN Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 31 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 110 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L1548 GLN B 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.193147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.150936 restraints weight = 14210.448| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.27 r_work: 0.3209 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13589 Z= 0.158 Angle : 0.498 6.857 19375 Z= 0.298 Chirality : 0.034 0.133 2173 Planarity : 0.003 0.040 1621 Dihedral : 28.331 148.351 3773 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.97 % Allowed : 13.63 % Favored : 85.40 % 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: 1.09 (0.29), residues: 964 helix: 2.55 (0.23), residues: 547 sheet: -0.98 (0.97), residues: 28 loop : -2.00 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L1562 HIS 0.003 0.001 HIS D 82 PHE 0.016 0.001 PHE L1589 TYR 0.009 0.001 TYR H 42 ARG 0.007 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.195 Fit side-chains REVERT: L 1487 LYS cc_start: 0.3595 (tptp) cc_final: 0.2850 (mtpp) REVERT: L 1504 LEU cc_start: 0.3514 (tt) cc_final: 0.2794 (tp) REVERT: L 1582 GLU cc_start: 0.6265 (mt-10) cc_final: 0.5695 (tp30) REVERT: L 1606 PHE cc_start: 0.6827 (m-10) cc_final: 0.6393 (m-10) REVERT: A 42 ARG cc_start: 0.8476 (mmt-90) cc_final: 0.8085 (mmm160) REVERT: A 115 LYS cc_start: 0.7284 (mttp) cc_final: 0.7028 (mtmm) REVERT: B 92 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7821 (ttp80) REVERT: G 36 LYS cc_start: 0.8382 (tttt) cc_final: 0.7777 (mmtm) outliers start: 8 outliers final: 5 residues processed: 152 average time/residue: 0.4031 time to fit residues: 80.0012 Evaluate side-chains 149 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 113 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.188664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145245 restraints weight = 14041.238| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.27 r_work: 0.3116 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13589 Z= 0.244 Angle : 0.548 8.633 19375 Z= 0.321 Chirality : 0.036 0.134 2173 Planarity : 0.004 0.040 1621 Dihedral : 28.403 147.605 3773 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.72 % Allowed : 14.60 % Favored : 84.68 % 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: 0.86 (0.28), residues: 964 helix: 2.32 (0.23), residues: 547 sheet: -0.97 (0.97), residues: 28 loop : -2.04 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L1562 HIS 0.005 0.001 HIS D 82 PHE 0.015 0.002 PHE C 25 TYR 0.009 0.001 TYR D 121 ARG 0.008 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.115 Fit side-chains REVERT: L 1504 LEU cc_start: 0.3439 (tt) cc_final: 0.2755 (tp) REVERT: L 1582 GLU cc_start: 0.6315 (mt-10) cc_final: 0.5710 (tp30) REVERT: L 1606 PHE cc_start: 0.6961 (m-10) cc_final: 0.6526 (m-10) REVERT: A 42 ARG cc_start: 0.8553 (mmt-90) cc_final: 0.8141 (mmm160) REVERT: A 115 LYS cc_start: 0.7708 (mttp) cc_final: 0.7415 (mtmm) REVERT: B 27 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8239 (mm-40) REVERT: B 92 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7934 (ttp80) outliers start: 6 outliers final: 5 residues processed: 147 average time/residue: 0.3787 time to fit residues: 72.5243 Evaluate side-chains 147 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.190405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145848 restraints weight = 14041.012| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.06 r_work: 0.3200 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13589 Z= 0.168 Angle : 0.525 8.622 19375 Z= 0.312 Chirality : 0.035 0.136 2173 Planarity : 0.004 0.041 1621 Dihedral : 28.376 148.215 3773 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.72 % Allowed : 14.23 % Favored : 85.04 % 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: 1.02 (0.28), residues: 964 helix: 2.46 (0.23), residues: 547 sheet: -0.98 (1.12), residues: 18 loop : -1.97 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L1562 HIS 0.004 0.001 HIS L1629 PHE 0.014 0.001 PHE L1589 TYR 0.023 0.001 TYR L1666 ARG 0.008 0.000 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.954 Fit side-chains REVERT: L 1487 LYS cc_start: 0.3513 (tptp) cc_final: 0.2823 (mtpp) REVERT: L 1504 LEU cc_start: 0.3388 (tt) cc_final: 0.2716 (tp) REVERT: L 1582 GLU cc_start: 0.6287 (mt-10) cc_final: 0.5705 (tp30) REVERT: L 1606 PHE cc_start: 0.6858 (m-10) cc_final: 0.6389 (m-10) REVERT: L 1666 TYR cc_start: 0.6952 (m-10) cc_final: 0.6696 (m-80) REVERT: A 42 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.8101 (mmm160) REVERT: A 115 LYS cc_start: 0.7490 (mttp) cc_final: 0.7229 (mtmm) REVERT: B 92 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7797 (ttp80) outliers start: 6 outliers final: 5 residues processed: 142 average time/residue: 0.3654 time to fit residues: 67.7008 Evaluate side-chains 144 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 50.1352 > 50: distance: 56 - 161: 6.340 distance: 75 - 101: 5.715 distance: 87 - 90: 3.173 distance: 88 - 93: 3.329 distance: 93 - 94: 3.627 distance: 94 - 95: 4.388 distance: 95 - 101: 6.818 distance: 96 - 126: 5.984 distance: 101 - 102: 6.004 distance: 102 - 103: 4.925 distance: 102 - 105: 6.331 distance: 103 - 104: 11.320 distance: 103 - 110: 17.025 distance: 105 - 106: 5.701 distance: 106 - 107: 3.688 distance: 110 - 111: 16.696 distance: 111 - 112: 22.905 distance: 111 - 114: 16.693 distance: 112 - 113: 3.511 distance: 112 - 119: 23.939 distance: 114 - 115: 48.518 distance: 115 - 116: 43.534 distance: 116 - 117: 21.339 distance: 116 - 118: 50.135 distance: 119 - 120: 12.926 distance: 120 - 121: 13.259 distance: 120 - 123: 7.573 distance: 121 - 122: 5.137 distance: 121 - 126: 9.781 distance: 123 - 124: 3.211 distance: 123 - 125: 5.222 distance: 126 - 127: 9.539 distance: 127 - 130: 3.491 distance: 128 - 136: 8.180 distance: 130 - 131: 4.194 distance: 136 - 137: 4.622 distance: 137 - 138: 6.909 distance: 138 - 139: 22.564 distance: 138 - 143: 30.268 distance: 140 - 141: 5.654 distance: 141 - 142: 3.452 distance: 143 - 144: 16.570 distance: 144 - 145: 8.850 distance: 144 - 147: 19.584 distance: 145 - 146: 6.277 distance: 145 - 151: 5.512 distance: 147 - 148: 14.473 distance: 148 - 149: 14.326 distance: 148 - 150: 5.571 distance: 151 - 152: 7.672 distance: 152 - 153: 6.994 distance: 152 - 155: 5.275 distance: 153 - 154: 3.224 distance: 153 - 158: 21.997 distance: 158 - 159: 42.439 distance: 159 - 160: 19.928 distance: 160 - 161: 20.942 distance: 160 - 162: 19.457