Starting phenix.real_space_refine on Wed Aug 5 23:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6q_29778/08_2026/8g6q_29778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6q_29778/08_2026/8g6q_29778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g6q_29778/08_2026/8g6q_29778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6q_29778/08_2026/8g6q_29778_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g6q_29778/08_2026/8g6q_29778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6q_29778/08_2026/8g6q_29778.map" } resolution = 3.41 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= 0.001 sd= 0.011 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 288 5.49 5 S 13 5.16 5 C 6947 2.51 5 N 2331 2.21 5 O 2906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12485 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU K 73 " occ=0.63 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.63 Time building chain proxies: 2.60, per 1000 atoms: 0.21 Number of scatterers: 12485 At special positions: 0 Unit cell: (125.13, 83.42, 118.34, 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 13 16.00 P 288 15.00 O 2906 8.00 N 2331 7.00 C 6947 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: 0.89 Conformation dependent library (CDL) restraints added in 415.0 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1546 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.1% alpha, 4.2% beta 140 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.988A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.320A 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: 3.576A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.578A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.654A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.600A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.598A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.807A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.806A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.640A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.630A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.540A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.565A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.675A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.644A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.537A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.577A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.748A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.880A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.702A pdb=" N TYR K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.913A 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 removed outlier: 3.657A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.033A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.062A 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 removed outlier: 3.972A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 16 415 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 4008 1.46 - 1.58: 5834 1.58 - 1.70: 576 1.70 - 1.82: 24 Bond restraints: 13293 Sorted by residual: bond pdb=" C3' DG I -30 " pdb=" C2' DG I -30 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC I -29 " pdb=" C2' DC I -29 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 13288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 18392 1.96 - 3.91: 754 3.91 - 5.87: 47 5.87 - 7.83: 3 7.83 - 9.78: 3 Bond angle restraints: 19199 Sorted by residual: angle pdb=" C3' DT J 13 " pdb=" O3' DT J 13 " pdb=" P DT J 14 " ideal model delta sigma weight residual 119.70 113.76 5.94 1.20e+00 6.94e-01 2.45e+01 angle pdb=" O4' DG I -68 " pdb=" C4' DG I -68 " pdb=" C3' DG I -68 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" N3 DT J -50 " pdb=" C4 DT J -50 " pdb=" O4 DT J -50 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT I 68 " pdb=" C4 DT I 68 " pdb=" O4 DT I 68 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 19194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.03: 5833 35.03 - 70.06: 1405 70.06 - 105.09: 23 105.09 - 140.12: 5 140.12 - 175.15: 1 Dihedral angle restraints: 7267 sinusoidal: 4874 harmonic: 2393 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 44.85 175.15 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ILE K 44 " pdb=" C ILE K 44 " pdb=" N PHE K 45 " pdb=" CA PHE K 45 " ideal model delta harmonic sigma weight residual 180.00 161.20 18.80 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 86.57 133.43 1 3.50e+01 8.16e-04 1.32e+01 ... (remaining 7264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2117 0.096 - 0.192: 73 0.192 - 0.287: 1 0.287 - 0.383: 0 0.383 - 0.479: 3 Chirality restraints: 2194 Sorted by residual: chirality pdb=" P DG J 12 " pdb=" OP1 DG J 12 " pdb=" OP2 DG J 12 " pdb=" O5' DG J 12 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" P DT J 13 " pdb=" OP1 DT J 13 " pdb=" OP2 DT J 13 " pdb=" O5' DT J 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" P DT J 14 " pdb=" OP1 DT J 14 " pdb=" OP2 DT J 14 " pdb=" O5' DT J 14 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 2191 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 81 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C ASN D 81 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN D 81 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS D 82 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 40 " 0.007 2.00e-02 2.50e+03 1.14e-02 2.92e+00 pdb=" N1 DC J 40 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DC J 40 " 0.023 2.00e-02 2.50e+03 pdb=" O2 DC J 40 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 40 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DC J 40 " 0.013 2.00e-02 2.50e+03 pdb=" N4 DC J 40 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 40 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 40 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 68 " 0.008 2.00e-02 2.50e+03 1.11e-02 2.75e+00 pdb=" N1 DC J 68 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 68 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC J 68 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC J 68 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 68 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 68 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 68 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC J 68 " -0.005 2.00e-02 2.50e+03 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 639 2.71 - 3.26: 10948 3.26 - 3.81: 22761 3.81 - 4.35: 26747 4.35 - 4.90: 39308 Nonbonded interactions: 100403 Sorted by model distance: nonbonded pdb=" O ARG A 129 " pdb=" NH1 ARG A 129 " model vdw 2.164 3.120 nonbonded pdb=" N GLU F 52 " pdb=" OE1 GLU F 52 " model vdw 2.217 3.120 nonbonded pdb=" N GLU H 102 " pdb=" OE1 GLU H 102 " model vdw 2.218 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.242 3.040 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.257 3.120 ... (remaining 100398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 135) selection = (chain 'E' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) 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=0.63 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: 1.340 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.006 0.039 13293 Z= 0.502 Angle : 0.763 9.784 19199 Z= 0.645 Chirality : 0.046 0.479 2194 Planarity : 0.004 0.033 1427 Dihedral : 27.964 175.148 5721 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.14 % Allowed : 28.47 % Favored : 71.39 % 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: 2.17 (0.30), residues: 807 helix: 2.70 (0.23), residues: 523 sheet: -0.32 (1.11), residues: 24 loop : -1.13 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 35 TYR 0.013 0.001 TYR A 54 PHE 0.007 0.001 PHE D 62 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.50 (13293) covalent geometry : angle 0.76314 / 0.64 (19199) hydrogen bonds : bond 0.10486 / 7.39 ( 772) hydrogen bonds : angle 3.96643 / 2.76 ( 1947) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7835 (ttp-170) REVERT: B 91 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8538 (tttt) REVERT: C 64 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 99 ARG cc_start: 0.7172 (mtt180) cc_final: 0.5961 (mtp85) REVERT: E 64 LYS cc_start: 0.7944 (mttt) cc_final: 0.7521 (tmtt) REVERT: E 73 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8793 (tm-30) REVERT: K 1 MET cc_start: 0.4568 (tmm) cc_final: 0.2265 (pmm) REVERT: K 60 ASN cc_start: 0.8614 (m-40) cc_final: 0.8287 (m-40) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.1367 time to fit residues: 29.8108 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN F 75 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.067740 restraints weight = 33145.541| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.70 r_work: 0.2876 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13293 Z= 0.162 Angle : 0.620 7.179 19199 Z= 0.372 Chirality : 0.042 0.237 2194 Planarity : 0.004 0.052 1427 Dihedral : 30.300 177.624 4085 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.59 % Allowed : 28.03 % Favored : 70.38 % 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: 2.16 (0.31), residues: 807 helix: 2.71 (0.23), residues: 530 sheet: -0.41 (1.10), residues: 24 loop : -1.30 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.009 0.001 TYR G 50 PHE 0.009 0.001 PHE H 67 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (13293) covalent geometry : angle 0.61971 / 0.37 (19199) hydrogen bonds : bond 0.05840 / 3.92 ( 772) hydrogen bonds : angle 3.34694 / 2.39 ( 1947) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8338 (tpt170) REVERT: B 35 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8259 (ttp-170) REVERT: B 91 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8839 (ttmt) REVERT: C 64 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8620 (tm-30) REVERT: C 99 ARG cc_start: 0.7498 (mtt180) cc_final: 0.6359 (mtp85) REVERT: E 64 LYS cc_start: 0.7912 (mttt) cc_final: 0.7644 (tmtt) REVERT: G 64 GLU cc_start: 0.8103 (tt0) cc_final: 0.7868 (tm-30) REVERT: H 82 LYS cc_start: 0.9127 (tptp) cc_final: 0.8908 (tptp) REVERT: K 1 MET cc_start: 0.4486 (tmm) cc_final: 0.3220 (ppp) REVERT: K 68 HIS cc_start: 0.8662 (t70) cc_final: 0.8406 (t70) outliers start: 11 outliers final: 6 residues processed: 148 average time/residue: 0.1307 time to fit residues: 26.6168 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 4.9990 chunk 98 optimal weight: 40.0000 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.099641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.066992 restraints weight = 33742.340| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.74 r_work: 0.2856 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13293 Z= 0.162 Angle : 0.598 7.461 19199 Z= 0.359 Chirality : 0.042 0.240 2194 Planarity : 0.004 0.049 1427 Dihedral : 30.318 177.930 4085 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.03 % Allowed : 26.45 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.31), residues: 807 helix: 2.64 (0.23), residues: 531 sheet: -0.43 (1.11), residues: 24 loop : -1.45 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.009 0.001 TYR D 37 PHE 0.009 0.001 PHE H 67 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (13293) covalent geometry : angle 0.59836 / 0.36 (19199) hydrogen bonds : bond 0.05786 / 3.85 ( 772) hydrogen bonds : angle 3.27022 / 2.35 ( 1947) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8305 (tp40) cc_final: 0.8072 (tp-100) REVERT: A 129 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8364 (tpt170) REVERT: B 35 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8224 (ttp-170) REVERT: C 64 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8644 (tm-30) REVERT: C 99 ARG cc_start: 0.7471 (mtt180) cc_final: 0.6377 (mtp85) REVERT: E 64 LYS cc_start: 0.7947 (mttt) cc_final: 0.7676 (tmtt) REVERT: G 64 GLU cc_start: 0.8107 (tt0) cc_final: 0.7850 (tm-30) REVERT: H 48 ASP cc_start: 0.9000 (p0) cc_final: 0.8791 (p0) REVERT: H 82 LYS cc_start: 0.9207 (tptp) cc_final: 0.8946 (tptp) REVERT: K 1 MET cc_start: 0.4592 (tmm) cc_final: 0.3481 (ppp) REVERT: K 60 ASN cc_start: 0.8623 (m-40) cc_final: 0.8417 (m-40) REVERT: K 68 HIS cc_start: 0.8622 (t70) cc_final: 0.8332 (t70) outliers start: 21 outliers final: 12 residues processed: 149 average time/residue: 0.1160 time to fit residues: 23.9561 Evaluate side-chains 139 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 30.0000 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066814 restraints weight = 33297.619| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.73 r_work: 0.2851 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13293 Z= 0.159 Angle : 0.593 7.653 19199 Z= 0.356 Chirality : 0.042 0.248 2194 Planarity : 0.004 0.049 1427 Dihedral : 30.305 178.424 4085 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.47 % Allowed : 26.45 % Favored : 70.09 % 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: 2.05 (0.31), residues: 807 helix: 2.66 (0.23), residues: 531 sheet: -0.43 (1.10), residues: 24 loop : -1.47 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.009 0.001 TYR D 37 PHE 0.009 0.001 PHE H 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (13293) covalent geometry : angle 0.59315 / 0.36 (19199) hydrogen bonds : bond 0.05745 / 3.82 ( 772) hydrogen bonds : angle 3.24823 / 2.34 ( 1947) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7542 (pp) REVERT: A 76 GLN cc_start: 0.8283 (tp40) cc_final: 0.8046 (tp-100) REVERT: B 35 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8235 (ttp-170) REVERT: C 64 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8658 (tm-30) REVERT: C 99 ARG cc_start: 0.7482 (mtt180) cc_final: 0.6503 (mtp-110) REVERT: H 31 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7110 (ptpp) REVERT: H 82 LYS cc_start: 0.9236 (tptp) cc_final: 0.9008 (tptp) REVERT: K 1 MET cc_start: 0.4822 (tmm) cc_final: 0.1662 (pmm) REVERT: K 60 ASN cc_start: 0.8509 (m-40) cc_final: 0.8273 (m-40) REVERT: K 68 HIS cc_start: 0.8604 (t70) cc_final: 0.8249 (t70) outliers start: 24 outliers final: 16 residues processed: 157 average time/residue: 0.1148 time to fit residues: 24.9131 Evaluate side-chains 144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN D 81 ASN E 125 GLN G 38 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.097484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.064430 restraints weight = 33286.328| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.69 r_work: 0.2799 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13293 Z= 0.204 Angle : 0.644 7.852 19199 Z= 0.377 Chirality : 0.044 0.255 2194 Planarity : 0.004 0.049 1427 Dihedral : 30.338 179.341 4085 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.62 % Allowed : 26.30 % Favored : 69.08 % 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: 1.84 (0.31), residues: 807 helix: 2.50 (0.23), residues: 533 sheet: -0.70 (1.05), residues: 25 loop : -1.55 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.015 0.002 TYR E 54 PHE 0.009 0.001 PHE B 61 HIS 0.012 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (13293) covalent geometry : angle 0.64372 / 0.38 (19199) hydrogen bonds : bond 0.06830 / 4.53 ( 772) hydrogen bonds : angle 3.43798 / 2.48 ( 1947) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8349 (tp40) cc_final: 0.8118 (tp-100) REVERT: A 129 ARG cc_start: 0.8858 (tpt90) cc_final: 0.8531 (tpt170) REVERT: B 35 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8211 (ttp80) REVERT: C 64 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8650 (tm-30) REVERT: C 99 ARG cc_start: 0.7483 (mtt180) cc_final: 0.6485 (mtp85) REVERT: D 103 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8483 (mp) REVERT: G 64 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8221 (tt0) REVERT: H 31 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7209 (pttp) REVERT: H 48 ASP cc_start: 0.9138 (p0) cc_final: 0.8884 (p0) REVERT: H 82 LYS cc_start: 0.9320 (tptp) cc_final: 0.9077 (tptp) REVERT: K 1 MET cc_start: 0.4969 (tmm) cc_final: 0.2532 (pmm) REVERT: K 15 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8575 (mm) REVERT: K 24 GLU cc_start: 0.9642 (tp30) cc_final: 0.9140 (mp0) REVERT: K 60 ASN cc_start: 0.8599 (m-40) cc_final: 0.8364 (m-40) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.1028 time to fit residues: 22.5014 Evaluate side-chains 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 103 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 0.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN E 125 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** 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 = 0.3719 r_free = 0.3719 target = 0.099691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067260 restraints weight = 33002.445| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.70 r_work: 0.2863 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13293 Z= 0.147 Angle : 0.590 9.759 19199 Z= 0.354 Chirality : 0.042 0.263 2194 Planarity : 0.004 0.050 1427 Dihedral : 30.282 178.968 4085 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.18 % Allowed : 28.32 % Favored : 68.50 % 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: 2.11 (0.31), residues: 807 helix: 2.71 (0.23), residues: 532 sheet: -0.57 (1.08), residues: 24 loop : -1.44 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.012 0.001 TYR D 80 PHE 0.010 0.001 PHE H 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.15 (13293) covalent geometry : angle 0.59017 / 0.35 (19199) hydrogen bonds : bond 0.05456 / 3.60 ( 772) hydrogen bonds : angle 3.21292 / 2.30 ( 1947) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8384 (tp40) cc_final: 0.8149 (tp-100) REVERT: B 35 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8073 (ttp80) REVERT: C 64 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8671 (tm-30) REVERT: C 99 ARG cc_start: 0.7432 (mtt180) cc_final: 0.6463 (mtp85) REVERT: H 31 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7225 (ptpp) REVERT: H 48 ASP cc_start: 0.9126 (p0) cc_final: 0.8877 (p0) REVERT: H 82 LYS cc_start: 0.9213 (tptp) cc_final: 0.9004 (tptp) REVERT: K 1 MET cc_start: 0.5035 (tmm) cc_final: 0.2366 (pmm) REVERT: K 24 GLU cc_start: 0.9595 (tp30) cc_final: 0.9091 (mp0) REVERT: K 60 ASN cc_start: 0.8535 (m-40) cc_final: 0.8290 (m-40) REVERT: K 68 HIS cc_start: 0.8572 (t70) cc_final: 0.8205 (t70) outliers start: 22 outliers final: 14 residues processed: 155 average time/residue: 0.1197 time to fit residues: 25.6147 Evaluate side-chains 149 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 64 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.098301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065516 restraints weight = 33473.701| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.71 r_work: 0.2820 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13293 Z= 0.186 Angle : 0.631 8.970 19199 Z= 0.370 Chirality : 0.043 0.258 2194 Planarity : 0.004 0.051 1427 Dihedral : 30.317 179.830 4085 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.76 % Allowed : 27.75 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.31), residues: 807 helix: 2.67 (0.23), residues: 532 sheet: -0.81 (1.00), residues: 25 loop : -1.53 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 42 TYR 0.010 0.002 TYR E 54 PHE 0.009 0.001 PHE H 67 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (13293) covalent geometry : angle 0.63142 / 0.37 (19199) hydrogen bonds : bond 0.06139 / 4.07 ( 772) hydrogen bonds : angle 3.38626 / 2.43 ( 1947) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8374 (tp40) cc_final: 0.8164 (tp-100) REVERT: A 129 ARG cc_start: 0.8839 (tpt90) cc_final: 0.8457 (tpt170) REVERT: B 35 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8110 (ttp80) REVERT: C 64 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8634 (tm-30) REVERT: C 99 ARG cc_start: 0.7460 (mtt180) cc_final: 0.6498 (mtp85) REVERT: E 125 GLN cc_start: 0.8608 (mt0) cc_final: 0.8380 (mt0) REVERT: G 64 GLU cc_start: 0.8109 (tt0) cc_final: 0.7863 (tm-30) REVERT: H 31 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7214 (ptpp) REVERT: H 48 ASP cc_start: 0.9137 (p0) cc_final: 0.8880 (p0) REVERT: H 82 LYS cc_start: 0.9234 (tptp) cc_final: 0.9002 (tptp) REVERT: K 1 MET cc_start: 0.5246 (tmm) cc_final: 0.2592 (pmm) REVERT: K 24 GLU cc_start: 0.9617 (tp30) cc_final: 0.9123 (mp0) REVERT: K 60 ASN cc_start: 0.8574 (m-40) cc_final: 0.8333 (m-40) REVERT: K 68 HIS cc_start: 0.8660 (t70) cc_final: 0.8301 (t70) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 0.1165 time to fit residues: 24.1969 Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064469 restraints weight = 32905.252| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.67 r_work: 0.2799 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13293 Z= 0.199 Angle : 0.653 9.058 19199 Z= 0.380 Chirality : 0.044 0.265 2194 Planarity : 0.004 0.051 1427 Dihedral : 30.340 179.480 4085 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.90 % Allowed : 27.75 % Favored : 68.35 % 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: 1.83 (0.30), residues: 807 helix: 2.54 (0.22), residues: 532 sheet: -0.33 (1.11), residues: 19 loop : -1.70 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.018 0.002 TYR H 80 PHE 0.009 0.001 PHE H 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (13293) covalent geometry : angle 0.65281 / 0.38 (19199) hydrogen bonds : bond 0.06599 / 4.37 ( 772) hydrogen bonds : angle 3.47364 / 2.50 ( 1947) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8407 (tp40) cc_final: 0.8205 (tp-100) REVERT: A 129 ARG cc_start: 0.8913 (tpt90) cc_final: 0.8520 (tpt170) REVERT: B 35 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8198 (mtm180) REVERT: C 64 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8643 (tm-30) REVERT: C 99 ARG cc_start: 0.7566 (mtt180) cc_final: 0.6674 (mtp85) REVERT: D 81 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7793 (t0) REVERT: H 31 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7222 (pttp) REVERT: H 48 ASP cc_start: 0.9164 (p0) cc_final: 0.8924 (p0) REVERT: H 82 LYS cc_start: 0.9275 (tptp) cc_final: 0.9035 (tptp) REVERT: K 1 MET cc_start: 0.5335 (tmm) cc_final: 0.2700 (pmm) REVERT: K 24 GLU cc_start: 0.9618 (tp30) cc_final: 0.9152 (mp0) REVERT: K 60 ASN cc_start: 0.8655 (m-40) cc_final: 0.8405 (m-40) REVERT: K 68 HIS cc_start: 0.8728 (t70) cc_final: 0.8376 (t70) outliers start: 27 outliers final: 20 residues processed: 151 average time/residue: 0.1303 time to fit residues: 27.4247 Evaluate side-chains 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 12 optimal weight: 0.0050 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 0.1980 chunk 78 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.0570 chunk 37 optimal weight: 0.0170 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.100179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067929 restraints weight = 32943.701| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.70 r_work: 0.2879 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13293 Z= 0.153 Angle : 0.617 10.775 19199 Z= 0.365 Chirality : 0.042 0.266 2194 Planarity : 0.004 0.050 1427 Dihedral : 30.292 179.921 4085 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.60 % Allowed : 28.76 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.31), residues: 807 helix: 2.64 (0.22), residues: 532 sheet: -0.34 (1.20), residues: 20 loop : -1.46 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 54 TYR 0.013 0.001 TYR D 37 PHE 0.011 0.001 PHE H 67 HIS 0.014 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (13293) covalent geometry : angle 0.61741 / 0.36 (19199) hydrogen bonds : bond 0.05175 / 3.40 ( 772) hydrogen bonds : angle 3.25133 / 2.32 ( 1947) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8360 (tp40) cc_final: 0.8136 (tp-100) REVERT: A 129 ARG cc_start: 0.8910 (tpt90) cc_final: 0.8460 (tpt170) REVERT: B 35 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8152 (mtm180) REVERT: C 64 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 99 ARG cc_start: 0.7448 (mtt180) cc_final: 0.6740 (mtp-110) REVERT: G 64 GLU cc_start: 0.8095 (tt0) cc_final: 0.7838 (tm-30) REVERT: H 31 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7108 (ptpp) REVERT: H 48 ASP cc_start: 0.9176 (p0) cc_final: 0.8923 (p0) REVERT: H 82 LYS cc_start: 0.9165 (tptp) cc_final: 0.8951 (tptp) REVERT: K 1 MET cc_start: 0.5199 (tmm) cc_final: 0.2481 (pmm) REVERT: K 24 GLU cc_start: 0.9582 (tp30) cc_final: 0.9128 (mp0) REVERT: K 60 ASN cc_start: 0.8398 (m-40) cc_final: 0.8143 (m-40) outliers start: 18 outliers final: 12 residues processed: 150 average time/residue: 0.1303 time to fit residues: 27.0342 Evaluate side-chains 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.099794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.067420 restraints weight = 33204.056| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.72 r_work: 0.2865 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13293 Z= 0.148 Angle : 0.620 12.820 19199 Z= 0.363 Chirality : 0.042 0.257 2194 Planarity : 0.004 0.050 1427 Dihedral : 30.309 178.906 4085 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.17 % Allowed : 30.20 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.31), residues: 807 helix: 2.63 (0.23), residues: 531 sheet: -0.36 (1.18), residues: 20 loop : -1.47 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 42 TYR 0.029 0.002 TYR F 88 PHE 0.009 0.001 PHE H 67 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (13293) covalent geometry : angle 0.62046 / 0.36 (19199) hydrogen bonds : bond 0.05219 / 3.46 ( 772) hydrogen bonds : angle 3.32491 / 2.37 ( 1947) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8377 (tp40) cc_final: 0.8162 (tp-100) REVERT: A 129 ARG cc_start: 0.8926 (tpt90) cc_final: 0.8483 (tpt170) REVERT: B 35 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8187 (mtm180) REVERT: C 64 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8625 (tm-30) REVERT: C 99 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6736 (mtp-110) REVERT: E 125 GLN cc_start: 0.8546 (mt0) cc_final: 0.8287 (mt0) REVERT: G 64 GLU cc_start: 0.8060 (tt0) cc_final: 0.7837 (tm-30) REVERT: H 31 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7114 (ptpp) REVERT: H 48 ASP cc_start: 0.9156 (p0) cc_final: 0.8928 (p0) REVERT: H 81 ASN cc_start: 0.8369 (t0) cc_final: 0.7829 (t0) REVERT: H 82 LYS cc_start: 0.9161 (tptp) cc_final: 0.8933 (tptp) REVERT: K 1 MET cc_start: 0.5325 (tmm) cc_final: 0.2640 (pmm) REVERT: K 24 GLU cc_start: 0.9589 (tp30) cc_final: 0.9124 (mp0) REVERT: K 60 ASN cc_start: 0.8558 (m-40) cc_final: 0.8302 (m-40) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 0.1332 time to fit residues: 26.8411 Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 45 optimal weight: 0.0570 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.0030 chunk 35 optimal weight: 0.7980 overall best weight: 0.5108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.100914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.068819 restraints weight = 33151.266| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.71 r_work: 0.2900 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13293 Z= 0.145 Angle : 0.618 11.599 19199 Z= 0.362 Chirality : 0.041 0.257 2194 Planarity : 0.004 0.050 1427 Dihedral : 30.270 178.234 4085 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.46 % Allowed : 30.20 % Favored : 67.34 % 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: 1.94 (0.31), residues: 807 helix: 2.53 (0.23), residues: 532 sheet: -0.28 (1.17), residues: 20 loop : -1.40 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 42 TYR 0.013 0.001 TYR H 80 PHE 0.010 0.001 PHE H 67 HIS 0.014 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (13293) covalent geometry : angle 0.61812 / 0.36 (19199) hydrogen bonds : bond 0.04845 / 3.21 ( 772) hydrogen bonds : angle 3.31886 / 2.36 ( 1947) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.06 seconds wall clock time: 45 minutes 43.07 seconds (2743.07 seconds total)