Starting phenix.real_space_refine on Thu Aug 6 02:23:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ox1_17252/08_2026/8ox1_17252.map" } resolution = 2.7 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 293 5.49 5 S 18 5.16 5 C 7423 2.51 5 N 2502 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 13258 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 847 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "I" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2881 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 3064 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 511 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "M" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 575 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.73, per 1000 atoms: 0.21 Number of scatterers: 13258 At special positions: 0 Unit cell: (101.598, 117.292, 128.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 293 15.00 O 3022 8.00 N 2502 7.00 C 7423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 403.0 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 10 sheets defined 69.5% alpha, 2.7% beta 140 base pairs and 266 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.552A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.521A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.614A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.524A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.367A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 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 Processing helix chain 'L' and resid 385 through 398 removed outlier: 3.761A pdb=" N LEU L 391 " --> pdb=" O GLU L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 402 through 410 Processing helix chain 'L' and resid 416 through 431 Processing helix chain 'M' and resid 384 through 398 Processing helix chain 'M' and resid 402 through 410 Processing helix chain 'M' and resid 416 through 430 Processing sheet with id=AA1, 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=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: 6.738A 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: 7.099A 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 removed outlier: 6.685A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.919A 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: 7.279A 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 78 462 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 266 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1672 1.32 - 1.45: 5160 1.45 - 1.57: 6628 1.57 - 1.69: 582 1.69 - 1.82: 32 Bond restraints: 14074 Sorted by residual: bond pdb=" CA LYS L 411 " pdb=" CB LYS L 411 " ideal model delta sigma weight residual 1.525 1.438 0.087 1.29e-02 6.01e+03 4.58e+01 bond pdb=" O2P SEP M 434 " pdb=" P SEP M 434 " ideal model delta sigma weight residual 1.610 1.498 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.56e-02 4.11e+03 3.11e+01 bond pdb=" CA GLU L 386 " pdb=" CB GLU L 386 " ideal model delta sigma weight residual 1.530 1.444 0.086 1.56e-02 4.11e+03 3.04e+01 bond pdb=" O3P SEP M 434 " pdb=" P SEP M 434 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 14069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 19245 2.22 - 4.45: 900 4.45 - 6.67: 62 6.67 - 8.89: 6 8.89 - 11.12: 2 Bond angle restraints: 20215 Sorted by residual: angle pdb=" C GLU M 386 " pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta sigma weight residual 110.79 117.70 -6.91 1.66e+00 3.63e-01 1.73e+01 angle pdb=" O4' DA J -70 " pdb=" C4' DA J -70 " pdb=" C3' DA J -70 " ideal model delta sigma weight residual 106.00 103.55 2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" O5' DA J -53 " pdb=" C5' DA J -53 " pdb=" C4' DA J -53 " ideal model delta sigma weight residual 109.40 112.64 -3.24 8.00e-01 1.56e+00 1.64e+01 angle pdb=" N LEU M 391 " pdb=" CA LEU M 391 " pdb=" C LEU M 391 " ideal model delta sigma weight residual 111.07 106.75 4.32 1.07e+00 8.73e-01 1.63e+01 angle pdb=" N GLU L 386 " pdb=" CA GLU L 386 " pdb=" C GLU L 386 " ideal model delta sigma weight residual 111.11 115.85 -4.74 1.20e+00 6.94e-01 1.56e+01 ... (remaining 20210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.35: 6328 33.35 - 66.69: 1450 66.69 - 100.04: 11 100.04 - 133.39: 0 133.39 - 166.74: 2 Dihedral angle restraints: 7791 sinusoidal: 5168 harmonic: 2623 Sorted by residual: dihedral pdb=" C GLU M 386 " pdb=" N GLU M 386 " pdb=" CA GLU M 386 " pdb=" CB GLU M 386 " ideal model delta harmonic sigma weight residual -122.60 -133.69 11.09 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" C4' DT I 35 " pdb=" C3' DT I 35 " pdb=" O3' DT I 35 " pdb=" P DA I 36 " ideal model delta sinusoidal sigma weight residual 220.00 53.26 166.74 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " pdb=" O3' DA I 49 " pdb=" P DC I 50 " ideal model delta sinusoidal sigma weight residual 220.00 81.40 138.60 1 3.50e+01 8.16e-04 1.37e+01 ... (remaining 7788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 2024 0.102 - 0.204: 228 0.204 - 0.306: 11 0.306 - 0.409: 3 0.409 - 0.511: 1 Chirality restraints: 2267 Sorted by residual: chirality pdb=" CA GLU M 386 " pdb=" N GLU M 386 " pdb=" C GLU M 386 " pdb=" CB GLU M 386 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.52e+00 chirality pdb=" CA GLU L 386 " pdb=" N GLU L 386 " pdb=" C GLU L 386 " pdb=" CB GLU L 386 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA LYS L 429 " pdb=" N LYS L 429 " pdb=" C LYS L 429 " pdb=" CB LYS L 429 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2264 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -21 " 0.046 2.00e-02 2.50e+03 1.84e-02 1.01e+01 pdb=" N9 DG J -21 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG J -21 " -0.018 2.00e-02 2.50e+03 pdb=" N7 DG J -21 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DG J -21 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DG J -21 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG J -21 " 0.021 2.00e-02 2.50e+03 pdb=" N1 DG J -21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J -21 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG J -21 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DG J -21 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J -21 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 17 " -0.043 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" N1 DT I 17 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DT I 17 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DT I 17 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DT I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 17 " -0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 17 " -0.027 2.00e-02 2.50e+03 pdb=" C5 DT I 17 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 17 " 0.013 2.00e-02 2.50e+03 pdb=" C6 DT I 17 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -35 " 0.036 2.00e-02 2.50e+03 1.63e-02 7.30e+00 pdb=" N9 DA J -35 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DA J -35 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA J -35 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J -35 " 0.006 2.00e-02 2.50e+03 pdb=" N6 DA J -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA J -35 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA J -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA J -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA J -35 " -0.012 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3474 2.84 - 3.36: 11613 3.36 - 3.87: 26368 3.87 - 4.39: 30725 4.39 - 4.90: 42295 Nonbonded interactions: 114475 Sorted by model distance: nonbonded pdb=" OG1 THR E 45 " pdb=" OP1 DG J 70 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU M 387 " pdb=" N ASN M 413 " model vdw 2.336 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.349 3.040 nonbonded pdb=" O ARG L 380 " pdb=" NE2 GLN L 381 " model vdw 2.403 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.418 3.040 ... (remaining 114470 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' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 25 through 122) } ncs_group { reference = (chain 'L' and resid 377 through 433) selection = (chain 'M' and resid 377 through 433) } 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=0.00 max=1.00 mean=0.99 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: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 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 : 0.008 0.112 14074 Z= 0.550 Angle : 1.046 11.117 20215 Z= 0.701 Chirality : 0.068 0.511 2267 Planarity : 0.006 0.045 1542 Dihedral : 25.999 166.737 6097 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.12 % 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: 0.87 (0.26), residues: 879 helix: 1.24 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.002 ARG B 35 TYR 0.028 0.005 TYR G 50 PHE 0.020 0.005 PHE A 104 TRP 0.020 0.005 TRP M 385 HIS 0.008 0.002 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.55 (14074) covalent geometry : angle 1.04641 / 0.70 (20215) hydrogen bonds : bond 0.14424 / 9.83 ( 812) hydrogen bonds : angle 4.51158 / 3.20 ( 2065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8853 (mtt) cc_final: 0.8648 (mtp) REVERT: B 95 ARG cc_start: 0.8211 (mtt90) cc_final: 0.7915 (mtp85) REVERT: C 36 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8905 (mmtt) REVERT: D 30 ARG cc_start: 0.7535 (mmt90) cc_final: 0.6942 (mtp180) REVERT: D 39 TYR cc_start: 0.8633 (t80) cc_final: 0.8384 (t80) REVERT: D 96 ARG cc_start: 0.8831 (mtt-85) cc_final: 0.8505 (mtt-85) REVERT: E 56 LYS cc_start: 0.9195 (tttm) cc_final: 0.8801 (ttmt) REVERT: E 59 GLU cc_start: 0.8558 (pm20) cc_final: 0.8224 (pm20) REVERT: E 64 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8439 (mtmt) REVERT: G 11 ARG cc_start: 0.6623 (mtp-110) cc_final: 0.6320 (mtp180) REVERT: H 119 THR cc_start: 0.9121 (m) cc_final: 0.8911 (m) REVERT: L 380 ARG cc_start: 0.4563 (mmt90) cc_final: 0.4314 (ttm170) REVERT: L 406 ILE cc_start: 0.5969 (mt) cc_final: 0.5767 (tp) REVERT: L 423 ARG cc_start: 0.7788 (tpt170) cc_final: 0.7331 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.9027 time to fit residues: 170.8192 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.092232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067119 restraints weight = 25691.662| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.48 r_work: 0.2901 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14074 Z= 0.153 Angle : 0.647 9.574 20215 Z= 0.379 Chirality : 0.044 0.219 2267 Planarity : 0.004 0.040 1542 Dihedral : 30.107 170.145 4236 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.57 % Allowed : 8.79 % Favored : 89.63 % 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: 2.03 (0.27), residues: 879 helix: 2.11 (0.20), residues: 621 sheet: None (None), residues: 0 loop : -0.57 (0.31), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.016 0.001 TYR D 37 PHE 0.022 0.002 PHE A 104 TRP 0.021 0.002 TRP L 383 HIS 0.005 0.001 HIS M 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (14074) covalent geometry : angle 0.64720 / 0.38 (20215) hydrogen bonds : bond 0.05031 / 3.46 ( 812) hydrogen bonds : angle 3.17548 / 2.28 ( 2065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: D 30 ARG cc_start: 0.7357 (mmt90) cc_final: 0.7073 (mtp180) REVERT: D 31 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7832 (mmmm) REVERT: D 96 ARG cc_start: 0.8777 (mtt-85) cc_final: 0.8412 (mtt-85) REVERT: E 56 LYS cc_start: 0.9223 (tttm) cc_final: 0.8912 (ttmt) REVERT: E 64 LYS cc_start: 0.9086 (mmtp) cc_final: 0.8613 (mtmt) REVERT: F 22 LEU cc_start: 0.7921 (mt) cc_final: 0.7450 (mp) REVERT: L 423 ARG cc_start: 0.7765 (tpt170) cc_final: 0.7450 (tpm170) REVERT: M 431 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8372 (mtmm) outliers start: 12 outliers final: 3 residues processed: 155 average time/residue: 0.8143 time to fit residues: 134.3900 Evaluate side-chains 143 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain L residue 426 THR Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN M 402 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.091912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.066763 restraints weight = 25846.150| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.48 r_work: 0.2895 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14074 Z= 0.152 Angle : 0.621 9.020 20215 Z= 0.359 Chirality : 0.043 0.222 2267 Planarity : 0.004 0.040 1542 Dihedral : 30.361 172.967 4236 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.71 % Allowed : 11.15 % Favored : 87.14 % 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: 2.49 (0.27), residues: 879 helix: 2.44 (0.20), residues: 623 sheet: None (None), residues: 0 loop : -0.35 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.011 0.001 TYR D 37 PHE 0.010 0.001 PHE A 104 TRP 0.011 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (14074) covalent geometry : angle 0.62119 / 0.36 (20215) hydrogen bonds : bond 0.04683 / 3.22 ( 812) hydrogen bonds : angle 3.01045 / 2.15 ( 2065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8073 (mtp85) REVERT: C 73 ASN cc_start: 0.7969 (m-40) cc_final: 0.7724 (t160) REVERT: D 30 ARG cc_start: 0.7346 (mmt90) cc_final: 0.7060 (mtp180) REVERT: D 31 LYS cc_start: 0.8351 (mtpp) cc_final: 0.7825 (mmmm) REVERT: D 96 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8405 (mtt-85) REVERT: E 56 LYS cc_start: 0.9181 (tttm) cc_final: 0.8853 (ttmt) REVERT: E 59 GLU cc_start: 0.8569 (pm20) cc_final: 0.8209 (pm20) REVERT: E 64 LYS cc_start: 0.9071 (mmtp) cc_final: 0.8610 (mtmt) REVERT: F 22 LEU cc_start: 0.7889 (mt) cc_final: 0.7478 (mp) REVERT: G 15 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8301 (tttp) REVERT: H 119 THR cc_start: 0.9334 (m) cc_final: 0.9080 (m) REVERT: L 423 ARG cc_start: 0.7825 (tpt170) cc_final: 0.7307 (tpm170) REVERT: M 431 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8360 (mtmm) REVERT: M 432 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (mp) outliers start: 13 outliers final: 2 residues processed: 150 average time/residue: 0.7423 time to fit residues: 118.4779 Evaluate side-chains 139 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 432 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 88 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.065831 restraints weight = 25776.370| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.46 r_work: 0.2872 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14074 Z= 0.179 Angle : 0.635 8.653 20215 Z= 0.358 Chirality : 0.043 0.236 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.615 177.843 4236 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 11.02 % Favored : 87.01 % 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: 2.61 (0.27), residues: 879 helix: 2.46 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -0.13 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.011 0.001 TYR D 37 PHE 0.007 0.001 PHE E 78 TRP 0.006 0.001 TRP L 383 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (14074) covalent geometry : angle 0.63495 / 0.36 (20215) hydrogen bonds : bond 0.04693 / 3.24 ( 812) hydrogen bonds : angle 2.98399 / 2.13 ( 2065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8604 (tpt90) cc_final: 0.8297 (tpt-90) REVERT: B 95 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8113 (mtp85) REVERT: C 73 ASN cc_start: 0.8030 (m-40) cc_final: 0.7796 (t160) REVERT: D 30 ARG cc_start: 0.7397 (mmt90) cc_final: 0.7150 (mtp180) REVERT: D 31 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7819 (mmmm) REVERT: D 96 ARG cc_start: 0.8777 (mtt-85) cc_final: 0.8412 (mtt-85) REVERT: E 38 PRO cc_start: 0.8586 (Cg_exo) cc_final: 0.8359 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8616 (pm20) cc_final: 0.8263 (pm20) REVERT: E 64 LYS cc_start: 0.9074 (mmtp) cc_final: 0.8616 (mtmt) REVERT: F 22 LEU cc_start: 0.7919 (mt) cc_final: 0.7465 (mp) REVERT: G 15 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8283 (tttp) REVERT: H 119 THR cc_start: 0.9336 (m) cc_final: 0.9081 (m) REVERT: L 423 ARG cc_start: 0.7985 (tpt170) cc_final: 0.7607 (tpm170) REVERT: M 431 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8360 (mtmm) outliers start: 15 outliers final: 4 residues processed: 149 average time/residue: 0.7811 time to fit residues: 123.7077 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.090209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064797 restraints weight = 25932.819| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.47 r_work: 0.2846 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14074 Z= 0.225 Angle : 0.673 9.335 20215 Z= 0.372 Chirality : 0.045 0.244 2267 Planarity : 0.005 0.038 1542 Dihedral : 30.756 175.659 4236 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.36 % Allowed : 11.29 % Favored : 86.35 % 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: 2.52 (0.27), residues: 879 helix: 2.39 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -0.15 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.011 0.002 TYR D 37 PHE 0.008 0.002 PHE E 78 TRP 0.005 0.001 TRP M 403 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (14074) covalent geometry : angle 0.67312 / 0.37 (20215) hydrogen bonds : bond 0.05140 / 3.55 ( 812) hydrogen bonds : angle 3.05428 / 2.18 ( 2065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8907 (mttp) cc_final: 0.8474 (mtpp) REVERT: A 129 ARG cc_start: 0.8626 (tpt90) cc_final: 0.8291 (tpt-90) REVERT: B 95 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8195 (mtp85) REVERT: C 73 ASN cc_start: 0.8122 (m-40) cc_final: 0.7851 (t160) REVERT: D 30 ARG cc_start: 0.7388 (mmt90) cc_final: 0.7185 (mtp180) REVERT: D 31 LYS cc_start: 0.8348 (mtpp) cc_final: 0.7830 (mmmm) REVERT: E 38 PRO cc_start: 0.8566 (Cg_exo) cc_final: 0.8336 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8628 (pm20) cc_final: 0.8347 (pm20) REVERT: E 64 LYS cc_start: 0.9088 (mmtp) cc_final: 0.8641 (mtmt) REVERT: F 22 LEU cc_start: 0.7945 (mt) cc_final: 0.7534 (mp) REVERT: H 119 THR cc_start: 0.9331 (m) cc_final: 0.9079 (m) REVERT: L 423 ARG cc_start: 0.7966 (tpt170) cc_final: 0.7580 (tpm170) REVERT: M 428 LYS cc_start: 0.9399 (mtpp) cc_final: 0.9141 (mtmt) REVERT: M 431 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8365 (mtmm) outliers start: 18 outliers final: 9 residues processed: 145 average time/residue: 0.8142 time to fit residues: 125.4472 Evaluate side-chains 145 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain L residue 426 THR Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 20 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.0270 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.091397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.066092 restraints weight = 25700.521| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.48 r_work: 0.2877 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14074 Z= 0.134 Angle : 0.631 10.507 20215 Z= 0.355 Chirality : 0.043 0.236 2267 Planarity : 0.004 0.052 1542 Dihedral : 30.663 174.307 4236 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.84 % Allowed : 12.34 % Favored : 85.83 % 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: 2.72 (0.27), residues: 879 helix: 2.52 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -0.04 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 96 TYR 0.011 0.001 TYR D 37 PHE 0.007 0.001 PHE B 61 TRP 0.005 0.001 TRP L 424 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (14074) covalent geometry : angle 0.63124 / 0.36 (20215) hydrogen bonds : bond 0.04497 / 3.12 ( 812) hydrogen bonds : angle 2.98803 / 2.13 ( 2065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8586 (tpt90) cc_final: 0.8312 (tpt-90) REVERT: B 95 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8066 (mtp85) REVERT: C 73 ASN cc_start: 0.8014 (m-40) cc_final: 0.7794 (t160) REVERT: D 31 LYS cc_start: 0.8297 (mtpp) cc_final: 0.7761 (mmmm) REVERT: E 38 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8305 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8624 (pm20) cc_final: 0.8285 (pm20) REVERT: E 64 LYS cc_start: 0.9073 (mmtp) cc_final: 0.8626 (mtmt) REVERT: F 22 LEU cc_start: 0.7929 (mt) cc_final: 0.7495 (mp) REVERT: G 15 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8225 (tttp) REVERT: H 119 THR cc_start: 0.9317 (m) cc_final: 0.9068 (m) REVERT: M 428 LYS cc_start: 0.9401 (mtpp) cc_final: 0.9164 (mtmt) REVERT: M 431 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8374 (mtmm) outliers start: 14 outliers final: 5 residues processed: 149 average time/residue: 0.7893 time to fit residues: 125.0224 Evaluate side-chains 141 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 98 optimal weight: 10.9990 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.090561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065155 restraints weight = 25787.464| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.49 r_work: 0.2852 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 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 : 0.004 0.037 14074 Z= 0.203 Angle : 0.655 9.978 20215 Z= 0.364 Chirality : 0.044 0.240 2267 Planarity : 0.004 0.040 1542 Dihedral : 30.650 167.949 4236 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.36 % Allowed : 12.60 % 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 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: 2.67 (0.27), residues: 879 helix: 2.50 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.07 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 96 TYR 0.010 0.001 TYR D 37 PHE 0.007 0.001 PHE B 61 TRP 0.010 0.001 TRP L 383 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (14074) covalent geometry : angle 0.65450 / 0.36 (20215) hydrogen bonds : bond 0.04876 / 3.37 ( 812) hydrogen bonds : angle 3.00748 / 2.15 ( 2065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.354 Fit side-chains REVERT: A 64 LYS cc_start: 0.8896 (mttp) cc_final: 0.8462 (mtpp) REVERT: A 129 ARG cc_start: 0.8588 (tpt90) cc_final: 0.8310 (tpt-90) REVERT: B 95 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8134 (mtp85) REVERT: C 73 ASN cc_start: 0.8043 (m-40) cc_final: 0.7789 (t160) REVERT: D 31 LYS cc_start: 0.8238 (mtpp) cc_final: 0.7709 (mmmm) REVERT: E 38 PRO cc_start: 0.8521 (Cg_exo) cc_final: 0.8292 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8624 (pm20) cc_final: 0.8340 (pm20) REVERT: E 64 LYS cc_start: 0.9088 (mmtp) cc_final: 0.8639 (mtmt) REVERT: F 22 LEU cc_start: 0.7925 (mt) cc_final: 0.7516 (mp) REVERT: G 13 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7933 (tmtm) REVERT: G 104 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8892 (mm-40) REVERT: H 119 THR cc_start: 0.9319 (m) cc_final: 0.9070 (m) REVERT: L 423 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7606 (tpm170) REVERT: L 432 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7450 (mt) REVERT: M 431 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8352 (mtmm) outliers start: 18 outliers final: 10 residues processed: 146 average time/residue: 0.8063 time to fit residues: 124.8085 Evaluate side-chains 147 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** 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 = 0.3514 r_free = 0.3514 target = 0.091201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065927 restraints weight = 25607.098| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.46 r_work: 0.2877 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14074 Z= 0.140 Angle : 0.638 11.161 20215 Z= 0.357 Chirality : 0.042 0.234 2267 Planarity : 0.004 0.038 1542 Dihedral : 30.619 166.691 4236 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.23 % Allowed : 13.52 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.78 (0.27), residues: 879 helix: 2.58 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.03 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG L 423 TYR 0.011 0.001 TYR D 37 PHE 0.006 0.001 PHE B 61 TRP 0.008 0.001 TRP L 383 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (14074) covalent geometry : angle 0.63769 / 0.36 (20215) hydrogen bonds : bond 0.04526 / 3.14 ( 812) hydrogen bonds : angle 2.97894 / 2.13 ( 2065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.332 Fit side-chains REVERT: A 64 LYS cc_start: 0.8879 (mttp) cc_final: 0.8423 (mtpt) REVERT: A 129 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8311 (tpt-90) REVERT: B 95 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8091 (mtp85) REVERT: C 73 ASN cc_start: 0.7998 (m-40) cc_final: 0.7777 (t160) REVERT: D 31 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7683 (mmmm) REVERT: E 38 PRO cc_start: 0.8509 (Cg_exo) cc_final: 0.8281 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8616 (pm20) cc_final: 0.8277 (pm20) REVERT: E 64 LYS cc_start: 0.9077 (mmtp) cc_final: 0.8628 (mtmt) REVERT: F 22 LEU cc_start: 0.7915 (mt) cc_final: 0.7498 (mp) REVERT: G 13 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7923 (tmtm) REVERT: H 119 THR cc_start: 0.9307 (m) cc_final: 0.9058 (m) REVERT: L 423 ARG cc_start: 0.7763 (tpp-160) cc_final: 0.7534 (tpm170) REVERT: L 432 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7462 (mt) outliers start: 17 outliers final: 8 residues processed: 145 average time/residue: 0.7800 time to fit residues: 120.1032 Evaluate side-chains 144 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain L residue 432 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** 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 = 0.3485 r_free = 0.3485 target = 0.089543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064068 restraints weight = 25741.583| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.48 r_work: 0.2833 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14074 Z= 0.269 Angle : 0.712 9.964 20215 Z= 0.387 Chirality : 0.047 0.247 2267 Planarity : 0.005 0.041 1542 Dihedral : 30.803 153.419 4236 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.49 % Allowed : 13.65 % Favored : 83.86 % 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: 2.42 (0.27), residues: 879 helix: 2.31 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.19 (0.33), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 96 TYR 0.011 0.002 TYR A 54 PHE 0.009 0.002 PHE E 78 TRP 0.008 0.002 TRP L 383 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.27 (14074) covalent geometry : angle 0.71240 / 0.39 (20215) hydrogen bonds : bond 0.05544 / 3.81 ( 812) hydrogen bonds : angle 3.13152 / 2.23 ( 2065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.305 Fit side-chains REVERT: A 64 LYS cc_start: 0.8911 (mttp) cc_final: 0.8449 (mtpt) REVERT: A 129 ARG cc_start: 0.8556 (tpt90) cc_final: 0.8275 (tpt-90) REVERT: B 95 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8232 (mtp85) REVERT: C 73 ASN cc_start: 0.8152 (m-40) cc_final: 0.7840 (t160) REVERT: D 31 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7685 (mmmm) REVERT: E 38 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8254 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8660 (pm20) cc_final: 0.8365 (pm20) REVERT: E 64 LYS cc_start: 0.9107 (mmtp) cc_final: 0.8650 (mtmt) REVERT: F 22 LEU cc_start: 0.7916 (mt) cc_final: 0.7498 (mp) REVERT: G 13 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7964 (tmtm) REVERT: H 119 THR cc_start: 0.9326 (m) cc_final: 0.9073 (m) REVERT: L 422 ASP cc_start: 0.8219 (m-30) cc_final: 0.7971 (m-30) REVERT: L 432 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7483 (mt) REVERT: M 428 LYS cc_start: 0.9390 (mtpp) cc_final: 0.9164 (mtmt) REVERT: M 431 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8351 (mtmm) outliers start: 19 outliers final: 9 residues processed: 148 average time/residue: 0.7511 time to fit residues: 118.1269 Evaluate side-chains 148 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain L residue 432 LEU Chi-restraints excluded: chain M residue 381 GLN Chi-restraints excluded: chain M residue 431 LYS Chi-restraints excluded: chain M residue 433 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** 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 = 0.3511 r_free = 0.3511 target = 0.091000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065594 restraints weight = 25742.012| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.49 r_work: 0.2866 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14074 Z= 0.143 Angle : 0.663 11.619 20215 Z= 0.368 Chirality : 0.045 0.242 2267 Planarity : 0.005 0.046 1542 Dihedral : 30.713 149.251 4236 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.57 % Allowed : 14.96 % Favored : 83.46 % 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: 2.59 (0.27), residues: 879 helix: 2.43 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.07 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 96 TYR 0.013 0.001 TYR D 37 PHE 0.006 0.001 PHE B 61 TRP 0.018 0.002 TRP L 383 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14074) covalent geometry : angle 0.66295 / 0.37 (20215) hydrogen bonds : bond 0.04769 / 3.31 ( 812) hydrogen bonds : angle 3.05053 / 2.18 ( 2065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.320 Fit side-chains REVERT: A 64 LYS cc_start: 0.8880 (mttp) cc_final: 0.8429 (mtpt) REVERT: A 129 ARG cc_start: 0.8547 (tpt90) cc_final: 0.8280 (tpt-90) REVERT: B 95 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8138 (mtp85) REVERT: C 73 ASN cc_start: 0.8084 (m-40) cc_final: 0.7789 (t160) REVERT: D 31 LYS cc_start: 0.8164 (mtpp) cc_final: 0.7658 (mmmm) REVERT: E 38 PRO cc_start: 0.8471 (Cg_exo) cc_final: 0.8249 (Cg_endo) REVERT: E 59 GLU cc_start: 0.8623 (pm20) cc_final: 0.8341 (pm20) REVERT: E 64 LYS cc_start: 0.9082 (mmtp) cc_final: 0.8629 (mtmt) REVERT: F 22 LEU cc_start: 0.7908 (mt) cc_final: 0.7470 (mp) REVERT: G 13 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7953 (tmtm) REVERT: H 65 ASP cc_start: 0.9204 (t0) cc_final: 0.8994 (t0) REVERT: H 119 THR cc_start: 0.9316 (m) cc_final: 0.9074 (m) REVERT: L 422 ASP cc_start: 0.8174 (m-30) cc_final: 0.7925 (m-30) outliers start: 12 outliers final: 6 residues processed: 149 average time/residue: 0.7357 time to fit residues: 116.4074 Evaluate side-chains 145 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain H residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 25 ASN ** 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 = 0.3512 r_free = 0.3512 target = 0.091020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.065696 restraints weight = 25678.824| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.48 r_work: 0.2872 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14074 Z= 0.155 Angle : 0.657 11.117 20215 Z= 0.363 Chirality : 0.043 0.233 2267 Planarity : 0.004 0.039 1542 Dihedral : 30.621 144.343 4236 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.57 % Allowed : 14.57 % Favored : 83.86 % 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: 2.68 (0.27), residues: 879 helix: 2.50 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 96 TYR 0.011 0.001 TYR D 37 PHE 0.007 0.001 PHE B 61 TRP 0.021 0.002 TRP L 383 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (14074) covalent geometry : angle 0.65682 / 0.36 (20215) hydrogen bonds : bond 0.04560 / 3.18 ( 812) hydrogen bonds : angle 3.00978 / 2.15 ( 2065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5098.45 seconds wall clock time: 87 minutes 7.03 seconds (5227.03 seconds total)