Starting phenix.real_space_refine on Fri Aug 7 17:03:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9x_64891/08_2026/9v9x_64891.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9x_64891/08_2026/9v9x_64891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9x_64891/08_2026/9v9x_64891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9x_64891/08_2026/9v9x_64891.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9x_64891/08_2026/9v9x_64891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9x_64891/08_2026/9v9x_64891.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 12492 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 4 6.06 5 P 261 5.49 5 S 31 5.16 5 C 7329 2.51 5 N 2413 2.21 5 O 2929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12967 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2650 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "J" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2701 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "M" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11324 SG CYS M 18 68.322 27.302 74.368 1.00 87.86 S ATOM 11345 SG CYS M 21 66.501 23.691 74.782 1.00 91.25 S ATOM 11483 SG CYS M 39 67.371 25.331 71.398 1.00 84.00 S ATOM 11505 SG CYS M 42 64.635 26.612 73.703 1.00 79.81 S ATOM 11442 SG CYS M 34 72.170 40.310 73.263 1.00 70.21 S ATOM 11600 SG CYS M 53 69.547 39.027 75.864 1.00 75.91 S ATOM 11621 SG CYS M 56 72.035 41.765 76.776 1.00 77.53 S ATOM 12459 SG CYS N 51 86.666 40.305 55.283 1.00 82.41 S ATOM 12480 SG CYS N 54 90.368 39.650 55.452 1.00 85.68 S ATOM 12628 SG CYS N 72 88.333 40.299 58.665 1.00 76.71 S ATOM 12647 SG CYS N 75 89.159 43.116 56.273 1.00 73.13 S ATOM 12582 SG CYS N 67 73.604 41.275 55.667 1.00 66.35 S ATOM 12736 SG CYS N 87 76.232 42.863 53.330 1.00 72.14 S ATOM 12756 SG CYS N 90 72.500 43.016 52.483 1.00 72.57 S Time building chain proxies: 2.57, per 1000 atoms: 0.20 Number of scatterers: 12967 At special positions: 0 Unit cell: (124.3, 121, 118.8, 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 261 15.00 O 2929 8.00 N 2413 7.00 C 7329 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: 1.24 Conformation dependent library (CDL) restraints added in 482.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " Number of angles added : 18 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 65.2% alpha, 3.8% beta 125 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.982A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.996A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.638A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.435A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.682A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.544A pdb=" N MET D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.878A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.644A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.891A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.524A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 16 through 21' Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.411A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.041A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 13 Processing helix chain 'M' and resid 14 through 16 No H-bonds generated for 'chain 'M' and resid 14 through 16' Processing helix chain 'M' and resid 39 through 48 removed outlier: 3.629A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 Processing helix chain 'M' and resid 85 through 98 Processing helix chain 'M' and resid 110 through 115 removed outlier: 3.635A pdb=" N ARG M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 removed outlier: 4.381A pdb=" N GLN N 25 " --> pdb=" O LEU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 83 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.804A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.652A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.207A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.110A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.377A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 37 through 38 Processing sheet with id=AB3, first strand: chain 'N' and resid 70 through 72 444 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.70 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: 3127 1.34 - 1.46: 3777 1.46 - 1.58: 6253 1.58 - 1.69: 520 1.69 - 1.81: 46 Bond restraints: 13723 Sorted by residual: bond pdb=" C3' DT J 88 " pdb=" C2' DT J 88 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DT J 57 " pdb=" C2' DT J 57 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT I 104 " pdb=" C2' DT I 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC J 77 " pdb=" C2' DC J 77 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT J 79 " pdb=" C2' DT J 79 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 13718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 17516 0.99 - 1.98: 1553 1.98 - 2.98: 549 2.98 - 3.97: 27 3.97 - 4.96: 11 Bond angle restraints: 19656 Sorted by residual: angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 89 " pdb=" C4 DT J 89 " pdb=" O4 DT J 89 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT I 46 " pdb=" C4 DT I 46 " pdb=" O4 DT I 46 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.83e+01 ... (remaining 19651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 6418 35.41 - 70.82: 1173 70.82 - 106.22: 19 106.22 - 141.63: 2 141.63 - 177.04: 1 Dihedral angle restraints: 7613 sinusoidal: 4818 harmonic: 2795 Sorted by residual: dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 37.04 -177.04 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA ILE M 32 " pdb=" C ILE M 32 " pdb=" N GLU M 33 " pdb=" CA GLU M 33 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 85.73 134.27 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 7610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1692 0.044 - 0.089: 430 0.089 - 0.133: 126 0.133 - 0.178: 0 0.178 - 0.222: 1 Chirality restraints: 2249 Sorted by residual: chirality pdb=" CA GLU G 61 " pdb=" N GLU G 61 " pdb=" C GLU G 61 " pdb=" CB GLU G 61 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE M 31 " pdb=" N ILE M 31 " pdb=" C ILE M 31 " pdb=" CB ILE M 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2246 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO G 80 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO C 80 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 36 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C LYS G 36 " 0.019 2.00e-02 2.50e+03 pdb=" O LYS G 36 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY G 37 " -0.006 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 295 2.67 - 3.23: 10886 3.23 - 3.78: 22633 3.78 - 4.34: 28912 4.34 - 4.90: 43078 Nonbonded interactions: 105804 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.109 2.496 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.272 3.040 nonbonded pdb=" O CYS M 18 " pdb=" N GLY M 22 " model vdw 2.303 3.120 nonbonded pdb=" O LEU N 80 " pdb=" NZ LYS N 85 " model vdw 2.303 3.120 nonbonded pdb=" O SER N 41 " pdb=" OG SER N 44 " model vdw 2.308 3.040 ... (remaining 105799 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' selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = (chain 'B' and resid 23 through 100) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 120) selection = (chain 'H' and resid 31 through 120) } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.580 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.005 0.037 13739 Z= 0.466 Angle : 0.661 10.916 19674 Z= 0.584 Chirality : 0.042 0.222 2249 Planarity : 0.003 0.035 1584 Dihedral : 25.414 177.041 5803 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 938 helix: 2.71 (0.21), residues: 601 sheet: -0.27 (1.64), residues: 10 loop : -0.60 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 81 TYR 0.015 0.001 TYR A 54 PHE 0.007 0.001 PHE N 71 TRP 0.001 0.000 TRP N 17 HIS 0.003 0.000 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.47 (13723) covalent geometry : angle 0.65188 / 0.58 (19656) hydrogen bonds : bond 0.12125 / 8.03 ( 765) hydrogen bonds : angle 4.07004 / 2.88 ( 1952) metal coordination : bond 0.00797 / 0.44 ( 16) metal coordination : angle 3.73165 / 2.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.380 Fit side-chains REVERT: D 30 ARG cc_start: 0.4084 (ptp-110) cc_final: 0.3772 (mmt180) REVERT: D 39 TYR cc_start: 0.6427 (t80) cc_final: 0.6123 (t80) REVERT: D 105 LYS cc_start: 0.7302 (ptpt) cc_final: 0.7038 (ptpt) REVERT: M 17 MET cc_start: 0.4458 (pmm) cc_final: 0.2713 (pmm) REVERT: M 60 VAL cc_start: 0.7224 (t) cc_final: 0.7018 (t) REVERT: N 65 LYS cc_start: 0.7703 (ptmm) cc_final: 0.7245 (mtpt) REVERT: N 106 PHE cc_start: 0.5470 (m-80) cc_final: 0.4616 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1419 time to fit residues: 31.7099 Evaluate side-chains 144 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.156543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116672 restraints weight = 24300.882| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.58 r_work: 0.3327 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13739 Z= 0.144 Angle : 0.582 8.534 19674 Z= 0.348 Chirality : 0.042 0.259 2249 Planarity : 0.004 0.035 1584 Dihedral : 28.883 175.760 3899 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.85 % Allowed : 6.96 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.28), residues: 938 helix: 2.70 (0.21), residues: 611 sheet: None (None), residues: 0 loop : -0.62 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 81 TYR 0.019 0.001 TYR A 54 PHE 0.007 0.001 PHE M 38 TRP 0.008 0.002 TRP N 17 HIS 0.003 0.001 HIS N 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (13723) covalent geometry : angle 0.57427 / 0.35 (19656) hydrogen bonds : bond 0.05334 / 3.78 ( 765) hydrogen bonds : angle 2.80494 / 2.02 ( 1952) metal coordination : bond 0.00692 / 0.43 ( 16) metal coordination : angle 3.18907 / 2.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.355 Fit side-chains REVERT: C 72 ASP cc_start: 0.6899 (m-30) cc_final: 0.6682 (t0) REVERT: D 39 TYR cc_start: 0.7220 (t80) cc_final: 0.6955 (t80) REVERT: F 91 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8551 (ttpp) REVERT: H 59 MET cc_start: 0.8749 (mmt) cc_final: 0.8354 (mmt) REVERT: H 90 GLU cc_start: 0.7533 (mp0) cc_final: 0.6863 (mp0) REVERT: M 17 MET cc_start: 0.3808 (pmm) cc_final: 0.2924 (pmm) REVERT: M 60 VAL cc_start: 0.7318 (t) cc_final: 0.7064 (t) REVERT: N 57 MET cc_start: 0.4925 (tpp) cc_final: 0.3410 (ttm) REVERT: N 65 LYS cc_start: 0.7213 (ptmm) cc_final: 0.6397 (mtmt) REVERT: N 106 PHE cc_start: 0.6204 (m-80) cc_final: 0.5809 (m-80) outliers start: 7 outliers final: 4 residues processed: 141 average time/residue: 0.1282 time to fit residues: 25.2291 Evaluate side-chains 137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 44 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 chunk 100 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.151673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109208 restraints weight = 23770.350| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.67 r_work: 0.3221 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13739 Z= 0.172 Angle : 0.620 7.185 19674 Z= 0.359 Chirality : 0.044 0.251 2249 Planarity : 0.005 0.037 1584 Dihedral : 29.513 177.085 3899 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.34 % Allowed : 9.65 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.27), residues: 938 helix: 2.40 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 89 TYR 0.029 0.002 TYR G 57 PHE 0.011 0.002 PHE N 106 TRP 0.011 0.003 TRP N 17 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (13723) covalent geometry : angle 0.61373 / 0.36 (19656) hydrogen bonds : bond 0.06372 / 4.45 ( 765) hydrogen bonds : angle 2.87353 / 2.06 ( 1952) metal coordination : bond 0.01087 / 0.75 ( 16) metal coordination : angle 2.91001 / 2.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.315 Fit side-chains REVERT: B 68 ASP cc_start: 0.8567 (m-30) cc_final: 0.8303 (m-30) REVERT: C 72 ASP cc_start: 0.7095 (m-30) cc_final: 0.6830 (t0) REVERT: H 90 GLU cc_start: 0.7677 (mp0) cc_final: 0.7018 (mp0) REVERT: N 57 MET cc_start: 0.4970 (tpp) cc_final: 0.3427 (ttm) REVERT: N 106 PHE cc_start: 0.6161 (m-80) cc_final: 0.5824 (m-10) outliers start: 11 outliers final: 7 residues processed: 133 average time/residue: 0.1196 time to fit residues: 22.5006 Evaluate side-chains 136 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 44 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 0.0060 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.0570 chunk 90 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 overall best weight: 1.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111051 restraints weight = 23623.130| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.50 r_work: 0.3236 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13739 Z= 0.138 Angle : 0.562 6.811 19674 Z= 0.329 Chirality : 0.041 0.237 2249 Planarity : 0.004 0.036 1584 Dihedral : 29.524 175.711 3899 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.34 % Allowed : 10.74 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.27), residues: 938 helix: 2.63 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -0.99 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 89 TYR 0.012 0.001 TYR M 46 PHE 0.009 0.001 PHE B 61 TRP 0.008 0.002 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (13723) covalent geometry : angle 0.55511 / 0.33 (19656) hydrogen bonds : bond 0.05396 / 3.80 ( 765) hydrogen bonds : angle 2.70626 / 1.95 ( 1952) metal coordination : bond 0.01195 / 0.84 ( 16) metal coordination : angle 2.92724 / 1.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.221 Fit side-chains REVERT: A 73 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: C 72 ASP cc_start: 0.7136 (m-30) cc_final: 0.6884 (t0) REVERT: M 70 ARG cc_start: 0.6621 (tpp-160) cc_final: 0.6188 (ttm110) REVERT: N 57 MET cc_start: 0.5039 (tpp) cc_final: 0.3551 (ttm) REVERT: N 65 LYS cc_start: 0.6605 (ptmm) cc_final: 0.5688 (mtmt) REVERT: N 106 PHE cc_start: 0.6146 (m-80) cc_final: 0.5593 (m-80) outliers start: 11 outliers final: 8 residues processed: 131 average time/residue: 0.1215 time to fit residues: 22.6413 Evaluate side-chains 137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 108 optimal weight: 0.0470 chunk 80 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.153572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112608 restraints weight = 24068.786| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.48 r_work: 0.3270 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13739 Z= 0.122 Angle : 0.527 6.429 19674 Z= 0.315 Chirality : 0.040 0.231 2249 Planarity : 0.003 0.047 1584 Dihedral : 29.498 175.612 3899 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.10 % Allowed : 10.99 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.28), residues: 938 helix: 2.77 (0.21), residues: 611 sheet: None (None), residues: 0 loop : -0.89 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 64 TYR 0.007 0.001 TYR D 39 PHE 0.008 0.001 PHE B 61 TRP 0.007 0.002 TRP N 17 HIS 0.002 0.000 HIS M 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.12 (13723) covalent geometry : angle 0.52093 / 0.31 (19656) hydrogen bonds : bond 0.04757 / 3.40 ( 765) hydrogen bonds : angle 2.58125 / 1.86 ( 1952) metal coordination : bond 0.00904 / 0.62 ( 16) metal coordination : angle 2.72543 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: C 72 ASP cc_start: 0.7006 (m-30) cc_final: 0.6788 (t0) REVERT: H 59 MET cc_start: 0.8748 (mmt) cc_final: 0.8346 (mmt) REVERT: H 102 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6610 (mt-10) REVERT: M 64 ARG cc_start: 0.6412 (ttp80) cc_final: 0.6198 (ttp80) REVERT: N 57 MET cc_start: 0.5090 (tpp) cc_final: 0.3793 (ttm) REVERT: N 65 LYS cc_start: 0.6720 (ptmm) cc_final: 0.5863 (mtmt) REVERT: N 106 PHE cc_start: 0.5957 (m-80) cc_final: 0.5555 (m-80) outliers start: 9 outliers final: 6 residues processed: 133 average time/residue: 0.1108 time to fit residues: 21.1246 Evaluate side-chains 137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 72 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 40.0000 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.153269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112102 restraints weight = 23819.429| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.56 r_work: 0.3265 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13739 Z= 0.122 Angle : 0.527 6.147 19674 Z= 0.314 Chirality : 0.040 0.233 2249 Planarity : 0.003 0.036 1584 Dihedral : 29.531 175.762 3899 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.22 % Allowed : 11.60 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.28), residues: 938 helix: 2.81 (0.21), residues: 611 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 81 TYR 0.007 0.001 TYR H 37 PHE 0.009 0.001 PHE B 61 TRP 0.007 0.001 TRP N 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.12 (13723) covalent geometry : angle 0.52121 / 0.31 (19656) hydrogen bonds : bond 0.04771 / 3.41 ( 765) hydrogen bonds : angle 2.55746 / 1.84 ( 1952) metal coordination : bond 0.00948 / 0.65 ( 16) metal coordination : angle 2.68083 / 1.66 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 72 ASP cc_start: 0.7010 (m-30) cc_final: 0.6788 (t0) REVERT: D 30 ARG cc_start: 0.2831 (mmt180) cc_final: 0.1878 (ptp90) REVERT: N 57 MET cc_start: 0.4927 (tpp) cc_final: 0.3720 (ttm) REVERT: N 65 LYS cc_start: 0.6912 (ptmm) cc_final: 0.6116 (mtmt) REVERT: N 106 PHE cc_start: 0.5924 (m-80) cc_final: 0.5578 (m-80) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.1136 time to fit residues: 21.4794 Evaluate side-chains 138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 50.0000 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 92 optimal weight: 30.0000 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.150895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108482 restraints weight = 23606.085| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.51 r_work: 0.3205 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13739 Z= 0.159 Angle : 0.586 6.410 19674 Z= 0.338 Chirality : 0.042 0.251 2249 Planarity : 0.004 0.036 1584 Dihedral : 29.750 176.421 3899 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.08 % Allowed : 11.97 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.27), residues: 938 helix: 2.56 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -1.07 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 128 TYR 0.011 0.001 TYR H 37 PHE 0.014 0.002 PHE N 106 TRP 0.010 0.003 TRP N 17 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (13723) covalent geometry : angle 0.58035 / 0.34 (19656) hydrogen bonds : bond 0.05892 / 4.13 ( 765) hydrogen bonds : angle 2.75052 / 1.98 ( 1952) metal coordination : bond 0.01366 / 0.94 ( 16) metal coordination : angle 2.74389 / 1.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.244 Fit side-chains REVERT: H 59 MET cc_start: 0.8763 (mmt) cc_final: 0.8376 (mmt) REVERT: M 17 MET cc_start: 0.2929 (OUTLIER) cc_final: 0.2636 (pmm) REVERT: N 65 LYS cc_start: 0.6640 (ptmm) cc_final: 0.5843 (mtmt) REVERT: N 106 PHE cc_start: 0.5955 (m-80) cc_final: 0.5669 (m-80) outliers start: 17 outliers final: 14 residues processed: 133 average time/residue: 0.1005 time to fit residues: 19.4865 Evaluate side-chains 142 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 70 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.151023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107412 restraints weight = 23479.633| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.76 r_work: 0.3187 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13739 Z= 0.146 Angle : 0.574 10.301 19674 Z= 0.332 Chirality : 0.041 0.237 2249 Planarity : 0.004 0.037 1584 Dihedral : 29.753 176.899 3899 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.47 % Allowed : 12.94 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.28), residues: 938 helix: 2.58 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 81 TYR 0.009 0.001 TYR H 37 PHE 0.011 0.001 PHE N 106 TRP 0.010 0.002 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (13723) covalent geometry : angle 0.56732 / 0.33 (19656) hydrogen bonds : bond 0.05482 / 3.87 ( 765) hydrogen bonds : angle 2.74059 / 1.99 ( 1952) metal coordination : bond 0.01314 / 0.89 ( 16) metal coordination : angle 2.85457 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.372 Fit side-chains REVERT: C 72 ASP cc_start: 0.6832 (m-30) cc_final: 0.6473 (t0) REVERT: H 59 MET cc_start: 0.8815 (mmt) cc_final: 0.8503 (mmt) REVERT: M 17 MET cc_start: 0.2889 (OUTLIER) cc_final: 0.2611 (pmm) REVERT: M 70 ARG cc_start: 0.6766 (tpp-160) cc_final: 0.6325 (ttm110) REVERT: N 57 MET cc_start: 0.5032 (tpp) cc_final: 0.4152 (tpp) REVERT: N 65 LYS cc_start: 0.6868 (ptmm) cc_final: 0.6038 (mtmt) REVERT: N 106 PHE cc_start: 0.6062 (m-80) cc_final: 0.5790 (m-80) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.1262 time to fit residues: 23.3982 Evaluate side-chains 135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 3.9990 chunk 97 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 40.0000 chunk 115 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 12 optimal weight: 5.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.151336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109270 restraints weight = 23668.671| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.49 r_work: 0.3223 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13739 Z= 0.134 Angle : 0.557 8.712 19674 Z= 0.325 Chirality : 0.041 0.236 2249 Planarity : 0.004 0.037 1584 Dihedral : 29.734 177.355 3899 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.59 % Allowed : 12.70 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.28), residues: 938 helix: 2.62 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 71 TYR 0.009 0.001 TYR H 37 PHE 0.010 0.001 PHE N 106 TRP 0.010 0.002 TRP N 17 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (13723) covalent geometry : angle 0.55109 / 0.32 (19656) hydrogen bonds : bond 0.05277 / 3.73 ( 765) hydrogen bonds : angle 2.69401 / 1.95 ( 1952) metal coordination : bond 0.01206 / 0.84 ( 16) metal coordination : angle 2.79394 / 1.73 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.366 Fit side-chains REVERT: C 72 ASP cc_start: 0.6812 (m-30) cc_final: 0.6534 (t0) REVERT: M 17 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.2634 (pmm) REVERT: M 70 ARG cc_start: 0.6758 (tpp-160) cc_final: 0.6329 (ttm110) REVERT: N 65 LYS cc_start: 0.6780 (ptmm) cc_final: 0.5952 (mtmt) REVERT: N 106 PHE cc_start: 0.6091 (m-80) cc_final: 0.5833 (m-80) outliers start: 13 outliers final: 12 residues processed: 130 average time/residue: 0.1276 time to fit residues: 23.6945 Evaluate side-chains 138 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 76 GLN Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 23 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN M 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108694 restraints weight = 23625.140| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.70 r_work: 0.3203 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13739 Z= 0.154 Angle : 0.576 9.034 19674 Z= 0.333 Chirality : 0.042 0.242 2249 Planarity : 0.004 0.037 1584 Dihedral : 29.774 178.169 3899 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.83 % Allowed : 12.58 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 938 helix: 2.55 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 89 TYR 0.010 0.001 TYR H 37 PHE 0.012 0.001 PHE N 106 TRP 0.011 0.003 TRP N 17 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (13723) covalent geometry : angle 0.56979 / 0.33 (19656) hydrogen bonds : bond 0.05563 / 3.91 ( 765) hydrogen bonds : angle 2.76287 / 2.00 ( 1952) metal coordination : bond 0.01327 / 0.91 ( 16) metal coordination : angle 2.76182 / 1.72 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.374 Fit side-chains REVERT: C 72 ASP cc_start: 0.6802 (m-30) cc_final: 0.6544 (t0) REVERT: M 17 MET cc_start: 0.2735 (OUTLIER) cc_final: 0.2417 (pmm) REVERT: M 70 ARG cc_start: 0.6949 (tpp-160) cc_final: 0.6378 (ttm110) REVERT: N 57 MET cc_start: 0.5126 (tpp) cc_final: 0.3547 (ttm) REVERT: N 65 LYS cc_start: 0.6858 (ptmm) cc_final: 0.6042 (mtmt) REVERT: N 106 PHE cc_start: 0.6076 (m-80) cc_final: 0.5822 (m-80) outliers start: 15 outliers final: 13 residues processed: 130 average time/residue: 0.1240 time to fit residues: 23.1407 Evaluate side-chains 139 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 76 GLN Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 99 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 102 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 40.0000 chunk 18 optimal weight: 0.3980 chunk 117 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN ** M 76 GLN ** 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 = 0.4080 r_free = 0.4080 target = 0.151824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110487 restraints weight = 23503.346| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.57 r_work: 0.3231 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13739 Z= 0.122 Angle : 0.548 8.920 19674 Z= 0.321 Chirality : 0.040 0.227 2249 Planarity : 0.003 0.037 1584 Dihedral : 29.718 177.398 3899 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.22 % Allowed : 13.55 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.28), residues: 938 helix: 2.69 (0.21), residues: 611 sheet: None (None), residues: 0 loop : -0.98 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE B 61 TRP 0.009 0.002 TRP N 17 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.12 (13723) covalent geometry : angle 0.54220 / 0.32 (19656) hydrogen bonds : bond 0.04999 / 3.57 ( 765) hydrogen bonds : angle 2.68047 / 1.94 ( 1952) metal coordination : bond 0.01134 / 0.81 ( 16) metal coordination : angle 2.74843 / 1.68 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.71 seconds wall clock time: 49 minutes 37.57 seconds (2977.57 seconds total)