Starting phenix.real_space_refine on Thu Jun 19 15:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scz_25043/06_2025/7scz_25043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scz_25043/06_2025/7scz_25043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7scz_25043/06_2025/7scz_25043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scz_25043/06_2025/7scz_25043.map" model { file = "/net/cci-nas-00/data/ceres_data/7scz_25043/06_2025/7scz_25043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scz_25043/06_2025/7scz_25043.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 S 19 5.16 5 C 7110 2.51 5 N 2388 2.21 5 O 2959 1.98 5 H 10435 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23205 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4682 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1684 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1667 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1536 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 11.28, per 1000 atoms: 0.49 Number of scatterers: 23205 At special positions: 0 Unit cell: (89.46, 121.41, 120.345, 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) S 19 16.00 P 294 15.00 O 2959 8.00 N 2388 7.00 C 7110 6.00 H 10435 1.00 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: 6.03 Conformation dependent library (CDL) restraints added in 1.3 seconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 11 sheets defined 70.7% alpha, 3.9% beta 146 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 11.64 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.793A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.988A 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: 3.642A 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 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.501A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.644A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.633A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) 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: 4.142A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 404 through 415 Processing helix chain 'K' and resid 433 through 439 Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 457 through 465 removed outlier: 3.766A pdb=" N ASP K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.967A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.647A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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: 6.649A 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: 6.725A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 'K' and resid 418 through 420 removed outlier: 6.351A pdb=" N CYS K 429 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 9.34 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.07: 2390 1.07 - 1.26: 9404 1.26 - 1.45: 5394 1.45 - 1.63: 6804 1.63 - 1.82: 33 Bond restraints: 24025 Sorted by residual: bond pdb=" N LEU K 478 " pdb=" H LEU K 478 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER K 479 " pdb=" H SER K 479 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C6 DC J 69 " pdb=" H6 DC J 69 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG G 88 " pdb="HH11 ARG G 88 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C6 DC I -58 " pdb=" H6 DC I -58 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 24020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 43131 6.26 - 12.51: 448 12.51 - 18.77: 1 18.77 - 25.02: 0 25.02 - 31.28: 3 Bond angle restraints: 43583 Sorted by residual: angle pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 77.72 31.28 3.00e+00 1.11e-01 1.09e+02 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 110.00 79.30 30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CB ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 79.95 29.05 3.00e+00 1.11e-01 9.38e+01 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 109.52 123.02 -13.50 1.55e+00 4.16e-01 7.58e+01 angle pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 110.00 120.05 -10.05 1.50e+00 4.44e-01 4.49e+01 ... (remaining 43578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8370 35.32 - 70.64: 1611 70.64 - 105.96: 39 105.96 - 141.28: 1 141.28 - 176.60: 3 Dihedral angle restraints: 10024 sinusoidal: 7285 harmonic: 2739 Sorted by residual: dihedral pdb=" C ARG F 17 " pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual -122.60 -142.09 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual 122.80 141.32 -18.52 0 2.50e+00 1.60e-01 5.49e+01 dihedral pdb=" CA SER K 431 " pdb=" C SER K 431 " pdb=" N THR K 432 " pdb=" CA THR K 432 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2105 0.163 - 0.326: 114 0.326 - 0.489: 12 0.489 - 0.652: 0 0.652 - 0.815: 1 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA ARG F 17 " pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CB ARG F 17 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C3' DG I -44 " pdb=" C4' DG I -44 " pdb=" O3' DG I -44 " pdb=" C2' DG I -44 " both_signs ideal model delta sigma weight residual False -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB THR B 82 " pdb=" CA THR B 82 " pdb=" OG1 THR B 82 " pdb=" CG2 THR B 82 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 38 " -0.301 2.00e-02 2.50e+03 1.63e-01 7.98e+02 pdb=" N1 DT J 38 " -0.094 2.00e-02 2.50e+03 pdb=" C2 DT J 38 " 0.051 2.00e-02 2.50e+03 pdb=" O2 DT J 38 " 0.285 2.00e-02 2.50e+03 pdb=" N3 DT J 38 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DT J 38 " -0.100 2.00e-02 2.50e+03 pdb=" O4 DT J 38 " -0.257 2.00e-02 2.50e+03 pdb=" C5 DT J 38 " 0.035 2.00e-02 2.50e+03 pdb=" C7 DT J 38 " 0.193 2.00e-02 2.50e+03 pdb=" C6 DT J 38 " 0.028 2.00e-02 2.50e+03 pdb=" H3 DT J 38 " 0.087 2.00e-02 2.50e+03 pdb=" H6 DT J 38 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 47 " -0.369 2.00e-02 2.50e+03 1.34e-01 6.26e+02 pdb=" N9 DG J 47 " 0.012 2.00e-02 2.50e+03 pdb=" C8 DG J 47 " 0.096 2.00e-02 2.50e+03 pdb=" N7 DG J 47 " 0.103 2.00e-02 2.50e+03 pdb=" C5 DG J 47 " 0.057 2.00e-02 2.50e+03 pdb=" C6 DG J 47 " -0.034 2.00e-02 2.50e+03 pdb=" O6 DG J 47 " -0.218 2.00e-02 2.50e+03 pdb=" N1 DG J 47 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DG J 47 " 0.077 2.00e-02 2.50e+03 pdb=" N2 DG J 47 " 0.084 2.00e-02 2.50e+03 pdb=" N3 DG J 47 " 0.091 2.00e-02 2.50e+03 pdb=" C4 DG J 47 " 0.080 2.00e-02 2.50e+03 pdb=" H8 DG J 47 " 0.085 2.00e-02 2.50e+03 pdb=" H1 DG J 47 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 55 " 0.349 2.00e-02 2.50e+03 1.42e-01 6.07e+02 pdb=" N1 DT J 55 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT J 55 " -0.108 2.00e-02 2.50e+03 pdb=" O2 DT J 55 " -0.200 2.00e-02 2.50e+03 pdb=" N3 DT J 55 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DT J 55 " 0.045 2.00e-02 2.50e+03 pdb=" O4 DT J 55 " 0.211 2.00e-02 2.50e+03 pdb=" C5 DT J 55 " -0.050 2.00e-02 2.50e+03 pdb=" C7 DT J 55 " -0.093 2.00e-02 2.50e+03 pdb=" C6 DT J 55 " -0.064 2.00e-02 2.50e+03 pdb=" H3 DT J 55 " 0.035 2.00e-02 2.50e+03 pdb=" H6 DT J 55 " -0.059 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1155 2.18 - 2.79: 36628 2.79 - 3.39: 62947 3.39 - 4.00: 89620 4.00 - 4.60: 128365 Nonbonded interactions: 318715 Sorted by model distance: nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.578 2.450 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.617 2.450 nonbonded pdb=" OD2 ASP D 68 " pdb=" HH TYR F 98 " model vdw 1.621 2.450 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.628 2.450 ... (remaining 318710 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 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.330 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 59.050 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.014 0.065 13590 Z= 0.757 Angle : 1.915 13.497 19596 Z= 1.269 Chirality : 0.088 0.815 2232 Planarity : 0.035 0.172 1456 Dihedral : 27.439 176.605 5861 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 832 helix: 0.25 (0.19), residues: 580 sheet: -0.58 (1.52), residues: 6 loop : -0.05 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.027 TRP K 481 HIS 0.014 0.004 HIS D 49 PHE 0.049 0.012 PHE D 70 TYR 0.124 0.021 TYR C 57 ARG 0.011 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.13010 ( 818) hydrogen bonds : angle 6.36587 ( 2050) covalent geometry : bond 0.01353 (13590) covalent geometry : angle 1.91481 (19596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8343 (t0) cc_final: 0.8024 (t0) REVERT: B 98 TYR cc_start: 0.8484 (m-10) cc_final: 0.8269 (m-10) REVERT: C 40 SER cc_start: 0.7653 (p) cc_final: 0.7293 (p) REVERT: C 90 ASP cc_start: 0.6952 (t70) cc_final: 0.6673 (t70) REVERT: D 89 ILE cc_start: 0.9265 (mt) cc_final: 0.8900 (mt) REVERT: E 97 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6935 (mt-10) REVERT: G 61 GLU cc_start: 0.8342 (tp30) cc_final: 0.8060 (tp30) REVERT: H 88 THR cc_start: 0.9138 (m) cc_final: 0.8860 (p) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.7748 time to fit residues: 309.1269 Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.095107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.066616 restraints weight = 67034.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069777 restraints weight = 23732.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071754 restraints weight = 13890.706| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13590 Z= 0.205 Angle : 0.715 5.344 19596 Z= 0.440 Chirality : 0.042 0.406 2232 Planarity : 0.005 0.045 1456 Dihedral : 31.313 172.155 4153 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.23 % Allowed : 12.15 % Favored : 85.61 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 832 helix: 1.99 (0.21), residues: 585 sheet: -1.89 (1.33), residues: 11 loop : -0.10 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP K 481 HIS 0.009 0.001 HIS F 75 PHE 0.020 0.002 PHE A 67 TYR 0.013 0.002 TYR F 98 ARG 0.005 0.001 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 818) hydrogen bonds : angle 3.45738 ( 2050) covalent geometry : bond 0.00442 (13590) covalent geometry : angle 0.71470 (19596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 73 GLU cc_start: 0.7911 (tp30) cc_final: 0.7641 (tp30) REVERT: A 108 ASN cc_start: 0.8827 (t0) cc_final: 0.8505 (t0) REVERT: B 74 GLU cc_start: 0.8802 (tt0) cc_final: 0.8173 (mt-10) REVERT: D 35 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6836 (mt-10) REVERT: E 50 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8102 (tt0) REVERT: E 73 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7925 (tm-30) REVERT: E 94 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7987 (tp30) REVERT: F 25 ASN cc_start: 0.8569 (m110) cc_final: 0.8299 (m110) REVERT: G 92 GLU cc_start: 0.8919 (mp0) cc_final: 0.8635 (mp0) REVERT: H 68 ASP cc_start: 0.8526 (t0) cc_final: 0.8230 (t0) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.6242 time to fit residues: 194.3612 Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.065367 restraints weight = 67836.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068341 restraints weight = 23843.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.070254 restraints weight = 13984.131| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13590 Z= 0.207 Angle : 0.647 5.025 19596 Z= 0.399 Chirality : 0.041 0.372 2232 Planarity : 0.004 0.048 1456 Dihedral : 31.023 171.142 4153 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.37 % Allowed : 14.53 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.28), residues: 832 helix: 2.41 (0.21), residues: 582 sheet: -2.05 (1.39), residues: 11 loop : -0.32 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 481 HIS 0.007 0.001 HIS F 75 PHE 0.013 0.001 PHE A 67 TYR 0.011 0.001 TYR G 57 ARG 0.004 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 818) hydrogen bonds : angle 3.22160 ( 2050) covalent geometry : bond 0.00443 (13590) covalent geometry : angle 0.64735 (19596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 108 ASN cc_start: 0.8900 (t0) cc_final: 0.8623 (t0) REVERT: B 74 GLU cc_start: 0.8896 (tt0) cc_final: 0.8235 (mt-10) REVERT: D 35 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7243 (mt-10) REVERT: D 71 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8241 (tm-30) REVERT: E 94 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7962 (tp30) REVERT: E 125 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8456 (mm-40) REVERT: F 25 ASN cc_start: 0.8505 (m110) cc_final: 0.8274 (m110) REVERT: G 92 GLU cc_start: 0.8967 (mp0) cc_final: 0.8612 (mp0) REVERT: H 93 GLU cc_start: 0.8225 (mp0) cc_final: 0.7357 (mp0) REVERT: K 409 LYS cc_start: 0.8211 (tttt) cc_final: 0.7979 (pttp) outliers start: 17 outliers final: 16 residues processed: 197 average time/residue: 0.6395 time to fit residues: 175.1452 Evaluate side-chains 193 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064805 restraints weight = 68931.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067769 restraints weight = 24596.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069666 restraints weight = 14527.829| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13590 Z= 0.207 Angle : 0.637 9.180 19596 Z= 0.389 Chirality : 0.041 0.362 2232 Planarity : 0.004 0.049 1456 Dihedral : 30.869 172.126 4153 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.93 % Allowed : 16.34 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.28), residues: 832 helix: 2.40 (0.21), residues: 582 sheet: -1.71 (1.44), residues: 11 loop : -0.31 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 481 HIS 0.005 0.001 HIS H 82 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.002 TYR G 57 ARG 0.006 0.000 ARG K 452 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 818) hydrogen bonds : angle 3.15264 ( 2050) covalent geometry : bond 0.00441 (13590) covalent geometry : angle 0.63691 (19596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 108 ASN cc_start: 0.8978 (t0) cc_final: 0.8573 (t0) REVERT: B 74 GLU cc_start: 0.8935 (tt0) cc_final: 0.8530 (mt-10) REVERT: D 35 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7397 (mt-10) REVERT: D 68 ASP cc_start: 0.8173 (t0) cc_final: 0.7885 (t0) REVERT: D 71 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8261 (tm-30) REVERT: E 50 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8285 (tt0) REVERT: H 93 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: H 113 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8864 (tp30) REVERT: K 409 LYS cc_start: 0.8312 (tttt) cc_final: 0.8061 (pttp) outliers start: 21 outliers final: 16 residues processed: 199 average time/residue: 0.5845 time to fit residues: 160.3312 Evaluate side-chains 191 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.063964 restraints weight = 69207.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066810 restraints weight = 24455.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068655 restraints weight = 14540.007| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13590 Z= 0.233 Angle : 0.629 5.291 19596 Z= 0.386 Chirality : 0.043 0.358 2232 Planarity : 0.004 0.049 1456 Dihedral : 30.750 172.120 4153 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.37 % Allowed : 17.60 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.28), residues: 832 helix: 2.46 (0.21), residues: 580 sheet: -1.60 (1.48), residues: 11 loop : -0.42 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS H 82 PHE 0.011 0.001 PHE C 25 TYR 0.013 0.002 TYR G 57 ARG 0.004 0.000 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 818) hydrogen bonds : angle 3.20932 ( 2050) covalent geometry : bond 0.00503 (13590) covalent geometry : angle 0.62874 (19596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8948 (tt0) cc_final: 0.8476 (mt-10) REVERT: D 35 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7513 (mt-10) REVERT: D 59 MET cc_start: 0.8662 (tpp) cc_final: 0.8360 (tpp) REVERT: D 68 ASP cc_start: 0.8181 (t0) cc_final: 0.7915 (t0) REVERT: D 71 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8373 (tm-30) REVERT: G 110 ASN cc_start: 0.8810 (t0) cc_final: 0.8229 (p0) REVERT: H 93 GLU cc_start: 0.8249 (mp0) cc_final: 0.7441 (mp0) REVERT: K 409 LYS cc_start: 0.8320 (tttt) cc_final: 0.8019 (pttm) outliers start: 17 outliers final: 15 residues processed: 189 average time/residue: 0.5958 time to fit residues: 158.9904 Evaluate side-chains 187 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.092114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.064171 restraints weight = 68667.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067075 restraints weight = 24813.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.068920 restraints weight = 14861.678| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13590 Z= 0.215 Angle : 0.620 4.908 19596 Z= 0.380 Chirality : 0.042 0.356 2232 Planarity : 0.004 0.050 1456 Dihedral : 30.665 172.704 4153 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.23 % Allowed : 18.16 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.28), residues: 832 helix: 2.52 (0.21), residues: 580 sheet: -1.38 (1.50), residues: 11 loop : -0.47 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.001 PHE K 458 TYR 0.011 0.001 TYR G 57 ARG 0.004 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 818) hydrogen bonds : angle 3.11704 ( 2050) covalent geometry : bond 0.00460 (13590) covalent geometry : angle 0.61990 (19596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8943 (tt0) cc_final: 0.8475 (mt-10) REVERT: D 35 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7490 (mt-10) REVERT: D 68 ASP cc_start: 0.8233 (t0) cc_final: 0.7913 (t0) REVERT: D 71 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8385 (tm-30) REVERT: E 50 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8323 (tt0) REVERT: E 120 MET cc_start: 0.8529 (mtm) cc_final: 0.8256 (mtm) REVERT: G 110 ASN cc_start: 0.8790 (t0) cc_final: 0.8257 (p0) REVERT: H 93 GLU cc_start: 0.8239 (mp0) cc_final: 0.7441 (mp0) REVERT: K 409 LYS cc_start: 0.8353 (tttt) cc_final: 0.8041 (pttm) outliers start: 16 outliers final: 16 residues processed: 193 average time/residue: 0.5824 time to fit residues: 154.9961 Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064659 restraints weight = 69755.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.067533 restraints weight = 24685.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069335 restraints weight = 14673.313| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13590 Z= 0.207 Angle : 0.615 4.990 19596 Z= 0.377 Chirality : 0.041 0.356 2232 Planarity : 0.004 0.050 1456 Dihedral : 30.581 173.006 4153 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.65 % Allowed : 18.16 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.28), residues: 832 helix: 2.55 (0.21), residues: 580 sheet: -1.05 (1.56), residues: 11 loop : -0.50 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.011 0.001 TYR G 57 ARG 0.006 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 818) hydrogen bonds : angle 3.06023 ( 2050) covalent geometry : bond 0.00443 (13590) covalent geometry : angle 0.61459 (19596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8822 (t0) cc_final: 0.8534 (t0) REVERT: B 74 GLU cc_start: 0.8898 (tt0) cc_final: 0.8438 (mt-10) REVERT: D 35 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7550 (mt-10) REVERT: D 47 GLN cc_start: 0.8664 (mt0) cc_final: 0.8409 (tt0) REVERT: D 68 ASP cc_start: 0.8219 (t0) cc_final: 0.7892 (t0) REVERT: D 71 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8391 (tm-30) REVERT: E 37 LYS cc_start: 0.8468 (pttm) cc_final: 0.8205 (pttt) REVERT: E 120 MET cc_start: 0.8556 (mtm) cc_final: 0.8291 (mtm) REVERT: G 84 GLN cc_start: 0.8555 (tp40) cc_final: 0.8293 (tp-100) REVERT: G 110 ASN cc_start: 0.8783 (t0) cc_final: 0.8305 (p0) REVERT: H 93 GLU cc_start: 0.8232 (mp0) cc_final: 0.7435 (mp0) REVERT: H 121 TYR cc_start: 0.8999 (t80) cc_final: 0.8777 (t80) REVERT: K 409 LYS cc_start: 0.8347 (tttt) cc_final: 0.8025 (pttm) outliers start: 19 outliers final: 14 residues processed: 197 average time/residue: 0.5707 time to fit residues: 155.2989 Evaluate side-chains 194 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN K 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.094318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.067240 restraints weight = 69186.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.070186 restraints weight = 23819.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.072039 restraints weight = 13959.005| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13590 Z= 0.160 Angle : 0.608 7.544 19596 Z= 0.370 Chirality : 0.038 0.357 2232 Planarity : 0.003 0.049 1456 Dihedral : 30.421 173.123 4153 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.54 % Allowed : 19.41 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.29), residues: 832 helix: 2.80 (0.21), residues: 580 sheet: -0.68 (1.73), residues: 11 loop : -0.27 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.002 0.000 HIS B 75 PHE 0.012 0.001 PHE A 67 TYR 0.018 0.001 TYR D 40 ARG 0.004 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 818) hydrogen bonds : angle 2.80196 ( 2050) covalent geometry : bond 0.00349 (13590) covalent geometry : angle 0.60794 (19596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8822 (t0) cc_final: 0.8556 (t0) REVERT: B 74 GLU cc_start: 0.8922 (tt0) cc_final: 0.8498 (mt-10) REVERT: D 35 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 47 GLN cc_start: 0.8604 (mt0) cc_final: 0.8365 (tt0) REVERT: D 68 ASP cc_start: 0.8240 (t0) cc_final: 0.7979 (t0) REVERT: D 71 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8330 (tm-30) REVERT: E 37 LYS cc_start: 0.8447 (pttm) cc_final: 0.8183 (pttt) REVERT: E 120 MET cc_start: 0.8491 (mtm) cc_final: 0.8209 (mtm) REVERT: G 38 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8150 (m110) REVERT: G 84 GLN cc_start: 0.8491 (tp40) cc_final: 0.8235 (tp-100) REVERT: G 110 ASN cc_start: 0.8728 (t0) cc_final: 0.8389 (p0) REVERT: H 59 MET cc_start: 0.8999 (tpp) cc_final: 0.8744 (tpp) REVERT: H 68 ASP cc_start: 0.8762 (t0) cc_final: 0.8530 (t0) REVERT: H 93 GLU cc_start: 0.8150 (mp0) cc_final: 0.7476 (mp0) REVERT: H 121 TYR cc_start: 0.8980 (t80) cc_final: 0.8738 (t80) REVERT: K 409 LYS cc_start: 0.8347 (tttt) cc_final: 0.8016 (pttp) outliers start: 11 outliers final: 10 residues processed: 192 average time/residue: 0.5793 time to fit residues: 154.7234 Evaluate side-chains 188 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 406 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.0370 chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.067658 restraints weight = 68987.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070613 restraints weight = 23689.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072465 restraints weight = 13870.737| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13590 Z= 0.158 Angle : 0.602 8.964 19596 Z= 0.367 Chirality : 0.038 0.354 2232 Planarity : 0.003 0.049 1456 Dihedral : 30.354 173.271 4153 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.98 % Allowed : 19.97 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.29), residues: 832 helix: 2.91 (0.21), residues: 580 sheet: -0.72 (1.70), residues: 11 loop : -0.20 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.002 0.000 HIS F 75 PHE 0.014 0.001 PHE A 67 TYR 0.015 0.001 TYR G 39 ARG 0.003 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 818) hydrogen bonds : angle 2.74999 ( 2050) covalent geometry : bond 0.00343 (13590) covalent geometry : angle 0.60233 (19596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8859 (t0) cc_final: 0.8586 (t0) REVERT: B 74 GLU cc_start: 0.8901 (tt0) cc_final: 0.8492 (mt-10) REVERT: C 84 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8454 (tp-100) REVERT: D 47 GLN cc_start: 0.8590 (mt0) cc_final: 0.8358 (tt0) REVERT: D 68 ASP cc_start: 0.8274 (t0) cc_final: 0.8021 (t0) REVERT: D 71 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8315 (tm-30) REVERT: E 37 LYS cc_start: 0.8444 (pttm) cc_final: 0.8168 (pttt) REVERT: E 120 MET cc_start: 0.8499 (mtm) cc_final: 0.8262 (mtm) REVERT: G 61 GLU cc_start: 0.8476 (tp30) cc_final: 0.8183 (tp30) REVERT: G 84 GLN cc_start: 0.8511 (tp40) cc_final: 0.8249 (tp-100) REVERT: G 110 ASN cc_start: 0.8699 (t0) cc_final: 0.8417 (p0) REVERT: H 68 ASP cc_start: 0.8736 (t0) cc_final: 0.8523 (t0) REVERT: H 93 GLU cc_start: 0.8129 (mp0) cc_final: 0.7462 (mp0) REVERT: H 121 TYR cc_start: 0.8983 (t80) cc_final: 0.8734 (t80) REVERT: K 409 LYS cc_start: 0.8363 (tttt) cc_final: 0.8026 (pttp) outliers start: 7 outliers final: 7 residues processed: 189 average time/residue: 0.5928 time to fit residues: 155.0147 Evaluate side-chains 187 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 180 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.067522 restraints weight = 69843.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.070514 restraints weight = 24323.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072350 restraints weight = 14338.891| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13590 Z= 0.163 Angle : 0.601 9.190 19596 Z= 0.366 Chirality : 0.039 0.354 2232 Planarity : 0.003 0.049 1456 Dihedral : 30.260 173.368 4153 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.98 % Allowed : 20.11 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.29), residues: 832 helix: 2.96 (0.21), residues: 580 sheet: -0.78 (1.63), residues: 11 loop : -0.12 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.003 0.000 HIS F 75 PHE 0.012 0.001 PHE A 67 TYR 0.013 0.001 TYR D 40 ARG 0.003 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 818) hydrogen bonds : angle 2.77067 ( 2050) covalent geometry : bond 0.00353 (13590) covalent geometry : angle 0.60131 (19596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 182 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9076 (m-80) cc_final: 0.8826 (m-80) REVERT: A 73 GLU cc_start: 0.7846 (tp30) cc_final: 0.7628 (tp30) REVERT: B 47 SER cc_start: 0.8843 (t) cc_final: 0.8438 (t) REVERT: B 74 GLU cc_start: 0.8896 (tt0) cc_final: 0.8518 (mt-10) REVERT: D 35 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7383 (mt-10) REVERT: D 47 GLN cc_start: 0.8614 (mt0) cc_final: 0.8404 (tt0) REVERT: D 68 ASP cc_start: 0.8280 (t0) cc_final: 0.8017 (t0) REVERT: D 71 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8326 (tm-30) REVERT: E 37 LYS cc_start: 0.8457 (pttm) cc_final: 0.8198 (pttt) REVERT: E 50 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8066 (tt0) REVERT: E 120 MET cc_start: 0.8537 (mtm) cc_final: 0.8248 (mtm) REVERT: G 61 GLU cc_start: 0.8460 (tp30) cc_final: 0.8130 (tp30) REVERT: G 64 GLU cc_start: 0.7770 (tp30) cc_final: 0.7508 (tp30) REVERT: G 84 GLN cc_start: 0.8505 (tp40) cc_final: 0.8246 (tp-100) REVERT: G 110 ASN cc_start: 0.8666 (t0) cc_final: 0.8437 (p0) REVERT: H 93 GLU cc_start: 0.8123 (mp0) cc_final: 0.7493 (mp0) REVERT: H 121 TYR cc_start: 0.8988 (t80) cc_final: 0.8743 (t80) REVERT: K 409 LYS cc_start: 0.8363 (tttt) cc_final: 0.8020 (pttp) outliers start: 7 outliers final: 6 residues processed: 187 average time/residue: 0.6107 time to fit residues: 158.1156 Evaluate side-chains 184 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 89 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.065591 restraints weight = 69932.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.068470 restraints weight = 24624.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070282 restraints weight = 14577.152| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13590 Z= 0.214 Angle : 0.627 9.188 19596 Z= 0.380 Chirality : 0.042 0.354 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.278 173.999 4153 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.84 % Allowed : 19.97 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.29), residues: 832 helix: 2.77 (0.21), residues: 581 sheet: -0.74 (1.61), residues: 11 loop : -0.16 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS B 75 PHE 0.013 0.001 PHE A 67 TYR 0.014 0.002 TYR B 88 ARG 0.003 0.000 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 818) hydrogen bonds : angle 2.99737 ( 2050) covalent geometry : bond 0.00463 (13590) covalent geometry : angle 0.62685 (19596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8500.32 seconds wall clock time: 145 minutes 26.41 seconds (8726.41 seconds total)