Starting phenix.real_space_refine on Thu Jul 2 19:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r1d_53505/07_2026/9r1d_53505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r1d_53505/07_2026/9r1d_53505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r1d_53505/07_2026/9r1d_53505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r1d_53505/07_2026/9r1d_53505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r1d_53505/07_2026/9r1d_53505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r1d_53505/07_2026/9r1d_53505.map" } resolution = 3.21 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= 0.012 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 230 5.49 5 S 20 5.16 5 C 5471 2.51 5 N 1861 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9880 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 679 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "D" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 685 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "E" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "G" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 685 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "H" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 692 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "I" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2375 Classifications: {'DNA': 115} Link IDs: {'rna3p': 114} Chain: "J" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2340 Classifications: {'DNA': 115} Link IDs: {'rna3p': 114} Time building chain proxies: 2.36, per 1000 atoms: 0.24 Number of scatterers: 9880 At special positions: 0 Unit cell: (80.56, 114.48, 117.66, 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 20 16.00 P 230 15.00 O 2298 8.00 N 1861 7.00 C 5471 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: 0.84 Conformation dependent library (CDL) restraints added in 182.4 milliseconds 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1246 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 7 sheets defined 78.0% alpha, 2.1% beta 107 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.633A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.531A pdb=" N ILE B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 74 removed outlier: 4.054A pdb=" N GLU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.707A pdb=" N ARG B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 44 through 73 removed outlier: 3.755A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 43 through 72 removed outlier: 3.558A pdb=" N ILE D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 90 removed outlier: 3.504A pdb=" N THR D 84 " --> pdb=" O ARG D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 110 removed outlier: 3.650A pdb=" N LYS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 101 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 81 removed outlier: 3.529A pdb=" N LEU E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 135 removed outlier: 3.606A pdb=" N ILE E 127 " --> pdb=" O PHE E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 28 through 39 Processing helix chain 'F' and resid 47 through 74 removed outlier: 4.228A pdb=" N GLU F 51 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.704A pdb=" N ARG F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 44 through 72 removed outlier: 3.656A pdb=" N ALA G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'H' and resid 25 through 37 Processing helix chain 'H' and resid 43 through 73 Processing helix chain 'H' and resid 78 through 90 removed outlier: 3.656A pdb=" N LEU H 82 " --> pdb=" O GLY H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 110 removed outlier: 4.258A pdb=" N HIS H 97 " --> pdb=" O ASP H 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.747A pdb=" N ARG A 86 " --> pdb=" O VAL B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.916A pdb=" N ARG C 42 " --> pdb=" O LEU D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 80 Processing sheet with id=AA5, first strand: chain 'E' and resid 86 through 87 removed outlier: 6.847A pdb=" N ARG E 86 " --> pdb=" O VAL F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.353A pdb=" N ARG G 42 " --> pdb=" O LEU H 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 371 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 278 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 107 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1178 1.32 - 1.44: 3889 1.44 - 1.56: 4950 1.56 - 1.69: 458 1.69 - 1.81: 36 Bond restraints: 10511 Sorted by residual: bond pdb=" C2 DG I -33 " pdb=" N2 DG I -33 " ideal model delta sigma weight residual 1.341 1.304 0.037 1.00e-02 1.00e+04 1.40e+01 bond pdb=" C4' DG J 48 " pdb=" O4' DG J 48 " ideal model delta sigma weight residual 1.446 1.409 0.037 1.00e-02 1.00e+04 1.36e+01 bond pdb=" C5' DA I -53 " pdb=" C4' DA I -53 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.27e+01 bond pdb=" C PRO D 91 " pdb=" O PRO D 91 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.30e-02 5.92e+03 1.16e+01 bond pdb=" C3' DC J 56 " pdb=" C2' DC J 56 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 ... (remaining 10506 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 13588 1.61 - 3.22: 1362 3.22 - 4.83: 176 4.83 - 6.44: 37 6.44 - 8.05: 21 Bond angle restraints: 15184 Sorted by residual: angle pdb=" O5' DA I -53 " pdb=" C5' DA I -53 " pdb=" C4' DA I -53 " ideal model delta sigma weight residual 109.40 114.49 -5.09 8.00e-01 1.56e+00 4.05e+01 angle pdb=" O5' DG J 48 " pdb=" C5' DG J 48 " pdb=" C4' DG J 48 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.21e+01 angle pdb=" O5' DG J 47 " pdb=" C5' DG J 47 " pdb=" C4' DG J 47 " ideal model delta sigma weight residual 109.40 113.84 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" O4' DG I -5 " pdb=" C4' DG I -5 " pdb=" C3' DG I -5 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" O5' DC J 49 " pdb=" C5' DC J 49 " pdb=" C4' DC J 49 " ideal model delta sigma weight residual 109.40 113.37 -3.97 8.00e-01 1.56e+00 2.47e+01 ... (remaining 15179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.32: 4193 25.32 - 50.63: 1155 50.63 - 75.95: 346 75.95 - 101.26: 3 101.26 - 126.58: 1 Dihedral angle restraints: 5698 sinusoidal: 3779 harmonic: 1919 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 93.42 126.58 1 3.50e+01 8.16e-04 1.25e+01 dihedral pdb=" C ARG D 73 " pdb=" N ARG D 73 " pdb=" CA ARG D 73 " pdb=" CB ARG D 73 " ideal model delta harmonic sigma weight residual -122.60 -131.26 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CA ILE D 36 " pdb=" C ILE D 36 " pdb=" N ASN D 37 " pdb=" CA ASN D 37 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1702 0.129 - 0.257: 39 0.257 - 0.386: 2 0.386 - 0.514: 0 0.514 - 0.643: 14 Chirality restraints: 1757 Sorted by residual: chirality pdb=" P DG I -56 " pdb=" OP1 DG I -56 " pdb=" OP2 DG I -56 " pdb=" O5' DG I -56 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DA I -55 " pdb=" OP1 DA I -55 " pdb=" OP2 DA I -55 " pdb=" O5' DA I -55 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" P DC I -54 " pdb=" OP1 DC I -54 " pdb=" OP2 DC I -54 " pdb=" O5' DC I -54 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 1754 not shown) Planarity restraints: 1113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 73 " 0.117 2.00e-02 2.50e+03 5.88e-02 6.91e+01 pdb=" CG TYR B 73 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR B 73 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR B 73 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 73 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 73 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 73 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 73 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -33 " 0.080 2.00e-02 2.50e+03 4.54e-02 6.17e+01 pdb=" N9 DG I -33 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DG I -33 " 0.018 2.00e-02 2.50e+03 pdb=" N7 DG I -33 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG I -33 " -0.029 2.00e-02 2.50e+03 pdb=" C6 DG I -33 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG I -33 " 0.045 2.00e-02 2.50e+03 pdb=" N1 DG I -33 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I -33 " -0.036 2.00e-02 2.50e+03 pdb=" N2 DG I -33 " 0.069 2.00e-02 2.50e+03 pdb=" N3 DG I -33 " -0.070 2.00e-02 2.50e+03 pdb=" C4 DG I -33 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 47 " -0.069 2.00e-02 2.50e+03 2.63e-02 2.07e+01 pdb=" N9 DG J 47 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG J 47 " 0.025 2.00e-02 2.50e+03 pdb=" N7 DG J 47 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J 47 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DG J 47 " -0.012 2.00e-02 2.50e+03 pdb=" O6 DG J 47 " -0.027 2.00e-02 2.50e+03 pdb=" N1 DG J 47 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DG J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG J 47 " 0.021 2.00e-02 2.50e+03 pdb=" C4 DG J 47 " 0.018 2.00e-02 2.50e+03 ... (remaining 1110 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1204 2.75 - 3.29: 9082 3.29 - 3.83: 19330 3.83 - 4.36: 22215 4.36 - 4.90: 32442 Nonbonded interactions: 84273 Sorted by model distance: nonbonded pdb=" O ASN D 37 " pdb=" OG SER D 38 " model vdw 2.219 3.040 nonbonded pdb=" O6 DG I 48 " pdb=" N1 DG J -49 " model vdw 2.228 3.120 nonbonded pdb=" NH2 ARG B 89 " pdb=" OD1 ASP H 56 " model vdw 2.292 3.120 nonbonded pdb=" O ASN D 37 " pdb=" OD1 ASN D 37 " model vdw 2.324 3.040 nonbonded pdb=" N ILE G 24 " pdb=" OE1 GLU G 56 " model vdw 2.331 3.120 ... (remaining 84268 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' and resid 23 through 98) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 104) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 23 through 110) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.790 Find NCS groups from input model: 0.120 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 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 0.044 10511 Z= 0.620 Angle : 1.029 8.055 15184 Z= 0.799 Chirality : 0.075 0.643 1757 Planarity : 0.006 0.059 1113 Dihedral : 26.896 126.577 4452 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.32), residues: 643 helix: 1.29 (0.23), residues: 495 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 75 TYR 0.117 0.007 TYR B 73 PHE 0.030 0.003 PHE D 53 TRP 0.005 0.001 TRP H 25 HIS 0.004 0.001 HIS D 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.62 (10511) covalent geometry : angle 1.02885 / 0.80 (15184) hydrogen bonds : bond 0.11530 / 7.64 ( 649) hydrogen bonds : angle 4.93020 / 3.45 ( 1657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.174 Fit side-chains REVERT: A 62 ASP cc_start: 0.7618 (t0) cc_final: 0.6994 (p0) REVERT: B 25 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7409 (ptt-90) REVERT: B 72 GLU cc_start: 0.8449 (tp30) cc_final: 0.8015 (tp30) REVERT: C 51 MET cc_start: 0.8082 (tpp) cc_final: 0.7648 (tpt) REVERT: D 73 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7782 (ttm-80) REVERT: G 92 ASP cc_start: 0.8344 (t0) cc_final: 0.7957 (t0) REVERT: H 96 LYS cc_start: 0.7921 (tttt) cc_final: 0.7636 (tttm) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1271 time to fit residues: 18.2426 Evaluate side-chains 95 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.0470 chunk 74 optimal weight: 10.0000 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101389 restraints weight = 13219.857| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.14 r_work: 0.3116 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10511 Z= 0.158 Angle : 0.620 9.217 15184 Z= 0.372 Chirality : 0.040 0.180 1757 Planarity : 0.004 0.031 1113 Dihedral : 30.163 125.709 3230 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.57 % Allowed : 12.66 % Favored : 84.77 % 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: 2.30 (0.31), residues: 643 helix: 2.24 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 79 TYR 0.024 0.002 TYR C 57 PHE 0.023 0.002 PHE F 86 TRP 0.006 0.001 TRP D 25 HIS 0.003 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (10511) covalent geometry : angle 0.61960 / 0.37 (15184) hydrogen bonds : bond 0.04734 / 3.12 ( 649) hydrogen bonds : angle 2.96948 / 2.12 ( 1657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7522 (t0) cc_final: 0.7005 (p0) REVERT: A 67 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7691 (mtp85) REVERT: B 25 ARG cc_start: 0.7734 (ptt90) cc_final: 0.7441 (ptt-90) REVERT: B 72 GLU cc_start: 0.8410 (tp30) cc_final: 0.8112 (tp30) REVERT: D 73 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7843 (ttm-80) REVERT: E 80 ASN cc_start: 0.8163 (m-40) cc_final: 0.7939 (t0) REVERT: F 73 TYR cc_start: 0.9061 (t80) cc_final: 0.8850 (t80) REVERT: G 92 ASP cc_start: 0.8618 (t70) cc_final: 0.8169 (t0) REVERT: H 59 GLU cc_start: 0.8559 (tp30) cc_final: 0.8340 (tp30) REVERT: H 96 LYS cc_start: 0.8029 (tttt) cc_final: 0.7762 (tttm) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1110 time to fit residues: 14.9452 Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 59 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 81 optimal weight: 10.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.2860 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.147951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098792 restraints weight = 13216.564| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.09 r_work: 0.3078 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10511 Z= 0.172 Angle : 0.608 8.751 15184 Z= 0.356 Chirality : 0.039 0.173 1757 Planarity : 0.004 0.035 1113 Dihedral : 30.603 125.164 3230 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.44 % Rotamer: Outliers : 3.67 % Allowed : 12.84 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.31), residues: 643 helix: 2.30 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -1.18 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 87 TYR 0.021 0.002 TYR C 57 PHE 0.018 0.002 PHE H 53 TRP 0.010 0.002 TRP D 25 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (10511) covalent geometry : angle 0.60803 / 0.36 (15184) hydrogen bonds : bond 0.04395 / 2.91 ( 649) hydrogen bonds : angle 2.81705 / 2.02 ( 1657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.183 Fit side-chains REVERT: A 62 ASP cc_start: 0.7664 (t0) cc_final: 0.7136 (p0) REVERT: B 25 ARG cc_start: 0.7742 (ptt90) cc_final: 0.7426 (ptt-90) REVERT: B 72 GLU cc_start: 0.8413 (tp30) cc_final: 0.8095 (tp30) REVERT: D 37 ASN cc_start: 0.8433 (t0) cc_final: 0.8040 (t0) REVERT: D 73 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7721 (ttm-80) REVERT: E 80 ASN cc_start: 0.8231 (m-40) cc_final: 0.7973 (t0) REVERT: F 75 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8518 (ttp-170) REVERT: G 92 ASP cc_start: 0.8644 (t70) cc_final: 0.8179 (t0) REVERT: H 73 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7782 (mtp85) REVERT: H 96 LYS cc_start: 0.7987 (tttt) cc_final: 0.7727 (tttm) outliers start: 20 outliers final: 12 residues processed: 101 average time/residue: 0.1109 time to fit residues: 14.5031 Evaluate side-chains 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 71 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.145671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096197 restraints weight = 13291.184| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.10 r_work: 0.3046 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10511 Z= 0.200 Angle : 0.622 8.787 15184 Z= 0.357 Chirality : 0.039 0.184 1757 Planarity : 0.004 0.047 1113 Dihedral : 30.758 126.913 3230 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.24 % Favored : 98.60 % Rotamer: Outliers : 3.67 % Allowed : 13.58 % Favored : 82.75 % 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: 2.26 (0.31), residues: 643 helix: 2.27 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 87 TYR 0.016 0.002 TYR C 57 PHE 0.018 0.002 PHE H 53 TRP 0.007 0.002 TRP H 25 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (10511) covalent geometry : angle 0.62245 / 0.36 (15184) hydrogen bonds : bond 0.04448 / 2.96 ( 649) hydrogen bonds : angle 2.83852 / 2.03 ( 1657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.253 Fit side-chains REVERT: A 62 ASP cc_start: 0.7639 (t0) cc_final: 0.7115 (p0) REVERT: A 128 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: B 25 ARG cc_start: 0.7840 (ptt90) cc_final: 0.7485 (ptt-90) REVERT: B 72 GLU cc_start: 0.8442 (tp30) cc_final: 0.8024 (tp30) REVERT: D 37 ASN cc_start: 0.8463 (t0) cc_final: 0.8020 (t0) REVERT: E 75 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6446 (mtm-85) REVERT: E 80 ASN cc_start: 0.8209 (m-40) cc_final: 0.7993 (t0) REVERT: E 136 GLU cc_start: 0.5400 (mt-10) cc_final: 0.5151 (mt-10) REVERT: F 75 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8479 (ttp-170) REVERT: G 92 ASP cc_start: 0.8663 (t70) cc_final: 0.8215 (t0) REVERT: H 96 LYS cc_start: 0.8020 (tttt) cc_final: 0.7759 (tttm) outliers start: 20 outliers final: 15 residues processed: 102 average time/residue: 0.1220 time to fit residues: 16.0418 Evaluate side-chains 102 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.148395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099141 restraints weight = 13281.970| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.12 r_work: 0.3083 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10511 Z= 0.136 Angle : 0.554 8.135 15184 Z= 0.329 Chirality : 0.037 0.169 1757 Planarity : 0.003 0.026 1113 Dihedral : 30.637 127.525 3230 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.24 % Favored : 98.60 % Rotamer: Outliers : 2.94 % Allowed : 15.23 % Favored : 81.83 % 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: 2.77 (0.32), residues: 643 helix: 2.60 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -1.08 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 87 TYR 0.023 0.002 TYR B 73 PHE 0.014 0.001 PHE H 53 TRP 0.005 0.001 TRP D 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (10511) covalent geometry : angle 0.55354 / 0.33 (15184) hydrogen bonds : bond 0.03951 / 2.58 ( 649) hydrogen bonds : angle 2.62720 / 1.87 ( 1657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.267 Fit side-chains REVERT: A 62 ASP cc_start: 0.7561 (t0) cc_final: 0.7153 (p0) REVERT: A 128 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: B 25 ARG cc_start: 0.7812 (ptt90) cc_final: 0.7475 (ptt-90) REVERT: B 72 GLU cc_start: 0.8406 (tp30) cc_final: 0.7734 (tt0) REVERT: D 37 ASN cc_start: 0.8478 (t0) cc_final: 0.7910 (t0) REVERT: E 80 ASN cc_start: 0.8193 (m-40) cc_final: 0.7983 (t0) REVERT: E 136 GLU cc_start: 0.5305 (mt-10) cc_final: 0.5034 (mt-10) REVERT: F 75 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8386 (ttp-170) REVERT: G 92 ASP cc_start: 0.8608 (t70) cc_final: 0.8286 (t0) REVERT: H 73 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7848 (mtp85) REVERT: H 96 LYS cc_start: 0.7996 (tttt) cc_final: 0.7736 (tttm) outliers start: 16 outliers final: 10 residues processed: 95 average time/residue: 0.1060 time to fit residues: 13.4521 Evaluate side-chains 93 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 88 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.148383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099160 restraints weight = 13294.448| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.13 r_work: 0.3086 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 10511 Z= 0.136 Angle : 0.553 7.794 15184 Z= 0.326 Chirality : 0.036 0.170 1757 Planarity : 0.003 0.025 1113 Dihedral : 30.598 126.878 3230 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.44 % Rotamer: Outliers : 3.67 % Allowed : 15.96 % Favored : 80.37 % 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: 2.76 (0.32), residues: 643 helix: 2.59 (0.22), residues: 499 sheet: None (None), residues: 0 loop : -1.07 (0.44), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.020 0.001 TYR B 73 PHE 0.015 0.001 PHE H 53 TRP 0.008 0.001 TRP D 25 HIS 0.003 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (10511) covalent geometry : angle 0.55306 / 0.33 (15184) hydrogen bonds : bond 0.03978 / 2.62 ( 649) hydrogen bonds : angle 2.61376 / 1.86 ( 1657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.180 Fit side-chains REVERT: A 62 ASP cc_start: 0.7518 (t0) cc_final: 0.7086 (p0) REVERT: A 115 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 128 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: B 25 ARG cc_start: 0.7790 (ptt90) cc_final: 0.7480 (ptt-90) REVERT: B 72 GLU cc_start: 0.8390 (tp30) cc_final: 0.7741 (tt0) REVERT: D 37 ASN cc_start: 0.8404 (t0) cc_final: 0.7832 (t0) REVERT: D 42 MET cc_start: 0.7881 (ptm) cc_final: 0.7555 (ptm) REVERT: D 73 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7411 (tpp-160) REVERT: E 136 GLU cc_start: 0.5515 (mt-10) cc_final: 0.5210 (mt-10) REVERT: F 75 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8354 (ttp-170) REVERT: G 92 ASP cc_start: 0.8541 (t70) cc_final: 0.8310 (t0) REVERT: H 96 LYS cc_start: 0.8055 (tttt) cc_final: 0.7789 (tttm) outliers start: 20 outliers final: 14 residues processed: 100 average time/residue: 0.1019 time to fit residues: 13.5655 Evaluate side-chains 101 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 73 ARG Chi-restraints excluded: chain H residue 88 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 24 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.146061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096535 restraints weight = 13316.402| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.13 r_work: 0.3050 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10511 Z= 0.179 Angle : 0.590 8.144 15184 Z= 0.339 Chirality : 0.037 0.176 1757 Planarity : 0.004 0.038 1113 Dihedral : 30.748 127.386 3230 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.22 % Allowed : 16.70 % Favored : 79.08 % 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: 2.44 (0.32), residues: 643 helix: 2.33 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -1.12 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 41 TYR 0.024 0.002 TYR B 73 PHE 0.016 0.002 PHE H 53 TRP 0.008 0.002 TRP H 25 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (10511) covalent geometry : angle 0.59035 / 0.34 (15184) hydrogen bonds : bond 0.04253 / 2.84 ( 649) hydrogen bonds : angle 2.71507 / 1.93 ( 1657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.169 Fit side-chains REVERT: A 62 ASP cc_start: 0.7513 (t0) cc_final: 0.7097 (p0) REVERT: A 115 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8245 (mp) REVERT: A 128 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: B 25 ARG cc_start: 0.7928 (ptt90) cc_final: 0.7598 (ptt-90) REVERT: B 72 GLU cc_start: 0.8420 (tp30) cc_final: 0.7992 (tp30) REVERT: D 37 ASN cc_start: 0.8511 (t0) cc_final: 0.7915 (t0) REVERT: D 42 MET cc_start: 0.8312 (ptm) cc_final: 0.7902 (ptm) REVERT: D 93 ASP cc_start: 0.8312 (t70) cc_final: 0.7947 (t0) REVERT: E 75 ARG cc_start: 0.7170 (tpp80) cc_final: 0.6469 (mtm-85) REVERT: E 136 GLU cc_start: 0.5606 (mt-10) cc_final: 0.5303 (mt-10) REVERT: F 75 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8373 (ttp-170) REVERT: G 92 ASP cc_start: 0.8586 (t70) cc_final: 0.8298 (t0) REVERT: H 96 LYS cc_start: 0.8008 (tttt) cc_final: 0.7739 (tttm) outliers start: 23 outliers final: 14 residues processed: 101 average time/residue: 0.1036 time to fit residues: 13.7352 Evaluate side-chains 103 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097288 restraints weight = 13241.631| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.10 r_work: 0.3062 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10511 Z= 0.167 Angle : 0.574 8.300 15184 Z= 0.332 Chirality : 0.037 0.181 1757 Planarity : 0.003 0.028 1113 Dihedral : 30.753 127.958 3230 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.40 % Favored : 98.44 % Rotamer: Outliers : 3.49 % Allowed : 17.98 % Favored : 78.53 % 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: 2.53 (0.32), residues: 643 helix: 2.38 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -1.05 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.019 0.002 TYR B 73 PHE 0.014 0.002 PHE H 53 TRP 0.006 0.001 TRP H 25 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 (10511) covalent geometry : angle 0.57447 / 0.33 (15184) hydrogen bonds : bond 0.04099 / 2.71 ( 649) hydrogen bonds : angle 2.66838 / 1.90 ( 1657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.235 Fit side-chains REVERT: A 62 ASP cc_start: 0.7530 (t0) cc_final: 0.7082 (p0) REVERT: A 115 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 128 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7602 (mt0) REVERT: B 25 ARG cc_start: 0.7945 (ptt90) cc_final: 0.7601 (ptt-90) REVERT: B 72 GLU cc_start: 0.8386 (tp30) cc_final: 0.7927 (tp30) REVERT: D 37 ASN cc_start: 0.8440 (t0) cc_final: 0.7858 (t0) REVERT: D 42 MET cc_start: 0.8313 (ptm) cc_final: 0.7682 (ptm) REVERT: D 93 ASP cc_start: 0.8290 (t70) cc_final: 0.7905 (t0) REVERT: E 75 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6475 (mtm-85) REVERT: F 75 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8340 (ttp-170) REVERT: G 92 ASP cc_start: 0.8573 (t70) cc_final: 0.8291 (t0) REVERT: H 96 LYS cc_start: 0.7981 (tttt) cc_final: 0.7709 (tttm) outliers start: 19 outliers final: 14 residues processed: 99 average time/residue: 0.1161 time to fit residues: 14.9270 Evaluate side-chains 104 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 110 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 72 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.148640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099354 restraints weight = 13306.692| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.11 r_work: 0.3092 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10511 Z= 0.131 Angle : 0.537 7.797 15184 Z= 0.318 Chirality : 0.035 0.177 1757 Planarity : 0.003 0.038 1113 Dihedral : 30.611 127.234 3230 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.94 % Allowed : 18.35 % Favored : 78.72 % 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: 2.84 (0.32), residues: 643 helix: 2.60 (0.22), residues: 500 sheet: None (None), residues: 0 loop : -0.83 (0.46), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 100 TYR 0.015 0.001 TYR F 73 PHE 0.012 0.001 PHE H 53 TRP 0.004 0.001 TRP H 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (10511) covalent geometry : angle 0.53680 / 0.32 (15184) hydrogen bonds : bond 0.03877 / 2.54 ( 649) hydrogen bonds : angle 2.57010 / 1.83 ( 1657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.272 Fit side-chains REVERT: A 62 ASP cc_start: 0.7528 (t0) cc_final: 0.7066 (p0) REVERT: A 128 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7553 (mt0) REVERT: B 25 ARG cc_start: 0.7860 (ptt90) cc_final: 0.7515 (ptt-90) REVERT: B 72 GLU cc_start: 0.8345 (tp30) cc_final: 0.7685 (tt0) REVERT: D 37 ASN cc_start: 0.8436 (t0) cc_final: 0.7843 (t0) REVERT: D 42 MET cc_start: 0.8063 (ptm) cc_final: 0.7731 (ptm) REVERT: D 93 ASP cc_start: 0.8276 (t70) cc_final: 0.7888 (t0) REVERT: E 136 GLU cc_start: 0.5404 (mt-10) cc_final: 0.5054 (mt-10) REVERT: F 75 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8265 (ttp-170) REVERT: H 73 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7711 (mtp85) REVERT: H 96 LYS cc_start: 0.7956 (tttt) cc_final: 0.7689 (tttm) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.1065 time to fit residues: 13.8924 Evaluate side-chains 99 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098809 restraints weight = 13206.125| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.10 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10511 Z= 0.145 Angle : 0.554 9.111 15184 Z= 0.323 Chirality : 0.036 0.182 1757 Planarity : 0.003 0.029 1113 Dihedral : 30.642 127.144 3230 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.09 % Favored : 98.76 % Rotamer: Outliers : 2.39 % Allowed : 19.45 % Favored : 78.17 % 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: 2.80 (0.32), residues: 643 helix: 2.57 (0.22), residues: 503 sheet: None (None), residues: 0 loop : -0.97 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 36 TYR 0.021 0.001 TYR B 73 PHE 0.013 0.002 PHE H 53 TRP 0.006 0.001 TRP H 25 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (10511) covalent geometry : angle 0.55360 / 0.32 (15184) hydrogen bonds : bond 0.03967 / 2.61 ( 649) hydrogen bonds : angle 2.58986 / 1.84 ( 1657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1286 Ramachandran restraints generated. 643 Oldfield, 0 Emsley, 643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.258 Fit side-chains REVERT: A 62 ASP cc_start: 0.7499 (t0) cc_final: 0.7052 (p0) REVERT: A 115 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 128 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 25 ARG cc_start: 0.7920 (ptt90) cc_final: 0.7580 (ptt-90) REVERT: B 72 GLU cc_start: 0.8381 (tp30) cc_final: 0.7735 (tt0) REVERT: D 37 ASN cc_start: 0.8407 (t0) cc_final: 0.7825 (t0) REVERT: D 42 MET cc_start: 0.8302 (ptm) cc_final: 0.7919 (ptm) REVERT: D 93 ASP cc_start: 0.8286 (t70) cc_final: 0.7891 (t0) REVERT: E 75 ARG cc_start: 0.7120 (tpp80) cc_final: 0.6465 (mtm-85) REVERT: E 136 GLU cc_start: 0.5305 (mt-10) cc_final: 0.4969 (mt-10) REVERT: F 75 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8280 (ttp-170) REVERT: H 73 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7717 (mtp85) REVERT: H 96 LYS cc_start: 0.7967 (tttt) cc_final: 0.7703 (tttm) outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 0.0994 time to fit residues: 12.1846 Evaluate side-chains 96 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.149409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100048 restraints weight = 13374.672| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.13 r_work: 0.3103 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10511 Z= 0.129 Angle : 0.532 8.787 15184 Z= 0.315 Chirality : 0.035 0.177 1757 Planarity : 0.003 0.031 1113 Dihedral : 30.569 126.929 3230 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.39 % Allowed : 19.27 % Favored : 78.35 % 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: 2.95 (0.32), residues: 643 helix: 2.69 (0.22), residues: 501 sheet: None (None), residues: 0 loop : -0.87 (0.46), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 36 TYR 0.021 0.001 TYR B 73 PHE 0.012 0.001 PHE H 53 TRP 0.005 0.001 TRP H 25 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.13 (10511) covalent geometry : angle 0.53233 / 0.32 (15184) hydrogen bonds : bond 0.03851 / 2.51 ( 649) hydrogen bonds : angle 2.53527 / 1.80 ( 1657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1536.35 seconds wall clock time: 26 minutes 53.64 seconds (1613.64 seconds total)