Starting phenix.real_space_refine on Wed May 14 21:18:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6q_29778/05_2025/8g6q_29778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6q_29778/05_2025/8g6q_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6q_29778/05_2025/8g6q_29778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6q_29778/05_2025/8g6q_29778.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6q_29778/05_2025/8g6q_29778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6q_29778/05_2025/8g6q_29778_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.25, per 1000 atoms: 0.58 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: 2.68 Conformation dependent library (CDL) restraints added in 931.7 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: 5.41 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: 4.84 Time building geometry restraints manager: 3.24 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=" N ALA E 114 " pdb=" CA ALA E 114 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.40e-02 5.10e+03 4.38e+00 bond pdb=" P DG J 12 " pdb=" OP2 DG J 12 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" P DT J 13 " pdb=" OP2 DT J 13 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" P DT J 14 " pdb=" OP2 DT J 14 " ideal model delta sigma weight residual 1.480 1.517 -0.037 2.00e-02 2.50e+03 3.39e+00 bond pdb=" P DT J 13 " pdb=" OP1 DT J 13 " ideal model delta sigma weight residual 1.480 1.516 -0.036 2.00e-02 2.50e+03 3.32e+00 ... (remaining 13288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 18787 1.96 - 3.91: 366 3.91 - 5.87: 40 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 120.20 113.76 6.44 1.50e+00 4.44e-01 1.84e+01 angle pdb=" C3' DC J 11 " pdb=" O3' DC J 11 " pdb=" P DG J 12 " ideal model delta sigma weight residual 120.20 114.93 5.27 1.50e+00 4.44e-01 1.23e+01 angle pdb=" N ASN D 81 " pdb=" CA ASN D 81 " pdb=" C ASN D 81 " ideal model delta sigma weight residual 112.25 107.80 4.45 1.36e+00 5.41e-01 1.07e+01 angle pdb=" C3' DG J 12 " pdb=" O3' DG J 12 " pdb=" P DT J 13 " ideal model delta sigma weight residual 120.20 115.50 4.70 1.50e+00 4.44e-01 9.83e+00 angle pdb=" CA ASN D 81 " pdb=" CB ASN D 81 " pdb=" CG ASN D 81 " ideal model delta sigma weight residual 112.60 115.72 -3.12 1.00e+00 1.00e+00 9.71e+00 ... (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 - 0.094: 2143 0.094 - 0.188: 46 0.188 - 0.281: 2 0.281 - 0.375: 0 0.375 - 0.469: 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 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.50e+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 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.36e+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 2.35 -2.80 -0.45 2.00e-01 2.50e+01 5.07e+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: 0.910 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.000 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.003 0.039 13293 Z= 0.163 Angle : 0.608 9.784 19199 Z= 0.352 Chirality : 0.037 0.469 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (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 HIS 0.005 0.001 HIS A 113 PHE 0.007 0.001 PHE D 62 TYR 0.013 0.001 TYR A 54 ARG 0.008 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.10486 ( 772) hydrogen bonds : angle 3.96643 ( 1947) covalent geometry : bond 0.00341 (13293) covalent geometry : angle 0.60830 (19199) *********************** 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 : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7836 (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: 0.5960 (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: 0.8794 (tm-30) REVERT: G 95 LYS cc_start: 0.8244 (tmmt) cc_final: 0.7748 (tmmt) REVERT: K 1 MET cc_start: 0.4568 (tmm) cc_final: 0.2263 (pmm) REVERT: K 60 ASN cc_start: 0.8614 (m-40) cc_final: 0.8286 (m-40) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2925 time to fit residues: 62.4767 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 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 = 0.3656 r_free = 0.3656 target = 0.095937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063141 restraints weight = 33108.583| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.66 r_work: 0.2765 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13293 Z= 0.276 Angle : 0.645 5.905 19199 Z= 0.376 Chirality : 0.037 0.180 2194 Planarity : 0.005 0.043 1427 Dihedral : 30.040 176.477 4085 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.75 % Allowed : 27.46 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.30), residues: 807 helix: 2.43 (0.22), residues: 525 sheet: -0.66 (1.06), residues: 24 loop : -1.57 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 75 PHE 0.011 0.002 PHE H 62 TYR 0.015 0.002 TYR G 50 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.07430 ( 772) hydrogen bonds : angle 3.58453 ( 1947) covalent geometry : bond 0.00638 (13293) covalent geometry : angle 0.64541 (19199) *********************** 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 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7741 (pp) REVERT: A 129 ARG cc_start: 0.8818 (tpt90) cc_final: 0.8484 (tpt170) REVERT: B 35 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8133 (ttp-170) REVERT: B 91 LYS cc_start: 0.9161 (ttpt) cc_final: 0.8947 (ttmt) REVERT: C 56 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8363 (tt0) REVERT: C 64 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8644 (tm-30) REVERT: C 99 ARG cc_start: 0.7516 (mtt180) cc_final: 0.6478 (mtp85) REVERT: E 64 LYS cc_start: 0.8073 (mttt) cc_final: 0.7847 (tmtt) REVERT: H 48 ASP cc_start: 0.9082 (p0) cc_final: 0.8870 (p0) REVERT: H 80 TYR cc_start: 0.7754 (m-10) cc_final: 0.7500 (m-10) REVERT: K 1 MET cc_start: 0.4872 (tmm) cc_final: 0.3956 (ppp) REVERT: K 15 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8552 (mm) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 0.3317 time to fit residues: 64.6074 Evaluate side-chains 134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 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 G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 0.4980 chunk 27 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN E 125 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 = 0.3699 r_free = 0.3699 target = 0.098468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.066009 restraints weight = 33133.121| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.70 r_work: 0.2830 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1378 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= 0.168 Angle : 0.554 5.364 19199 Z= 0.331 Chirality : 0.033 0.145 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.879 175.502 4085 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.75 % Allowed : 27.46 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.31), residues: 807 helix: 2.65 (0.22), residues: 532 sheet: -0.60 (1.08), residues: 24 loop : -1.47 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 79 PHE 0.011 0.001 PHE H 67 TYR 0.010 0.001 TYR D 37 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05322 ( 772) hydrogen bonds : angle 3.18031 ( 1947) covalent geometry : bond 0.00364 (13293) covalent geometry : angle 0.55354 (19199) *********************** 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 155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8067 (ttp80) REVERT: B 91 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8898 (tttt) REVERT: C 56 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8393 (tt0) REVERT: C 64 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 99 ARG cc_start: 0.7465 (mtt180) cc_final: 0.6645 (mtp-110) REVERT: D 81 ASN cc_start: 0.8017 (t0) cc_final: 0.7750 (t0) REVERT: G 64 GLU cc_start: 0.8132 (tt0) cc_final: 0.7839 (tm-30) REVERT: H 31 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7185 (ptpp) REVERT: K 1 MET cc_start: 0.4865 (tmm) cc_final: 0.1788 (pmm) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.2686 time to fit residues: 56.6901 Evaluate side-chains 136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 D residue 80 TYR 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 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066907 restraints weight = 33007.506| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.70 r_work: 0.2851 rms_B_bonded: 4.42 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 = 0.77 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 = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13293 Z= 0.159 Angle : 0.546 6.094 19199 Z= 0.326 Chirality : 0.033 0.148 2194 Planarity : 0.004 0.047 1427 Dihedral : 29.825 177.192 4085 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.05 % Allowed : 26.45 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.31), residues: 807 helix: 2.76 (0.22), residues: 531 sheet: -0.57 (1.07), residues: 24 loop : -1.51 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 68 PHE 0.011 0.001 PHE H 67 TYR 0.009 0.001 TYR D 80 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 772) hydrogen bonds : angle 3.10248 ( 1947) covalent geometry : bond 0.00340 (13293) covalent geometry : angle 0.54564 (19199) *********************** 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 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8882 (tpt90) cc_final: 0.8429 (tpt170) REVERT: B 35 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8063 (ttp80) REVERT: B 91 LYS cc_start: 0.9108 (ttpt) cc_final: 0.8845 (tttt) REVERT: C 56 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8419 (tt0) REVERT: C 64 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8598 (tm-30) REVERT: C 99 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6643 (mtp85) REVERT: D 81 ASN cc_start: 0.7984 (t0) cc_final: 0.7663 (t0) REVERT: G 64 GLU cc_start: 0.8119 (tt0) cc_final: 0.7876 (tm-30) REVERT: H 31 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7217 (pttp) REVERT: K 1 MET cc_start: 0.4855 (tmm) cc_final: 0.1700 (pmm) outliers start: 28 outliers final: 15 residues processed: 160 average time/residue: 0.2696 time to fit residues: 59.4083 Evaluate side-chains 148 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 118 THR 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 86 ILE Chi-restraints excluded: chain H residue 120 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3695 r_free = 0.3695 target = 0.098367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066352 restraints weight = 33124.616| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.66 r_work: 0.2827 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13293 Z= 0.185 Angle : 0.563 6.682 19199 Z= 0.335 Chirality : 0.034 0.151 2194 Planarity : 0.004 0.047 1427 Dihedral : 29.816 177.660 4085 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.34 % Allowed : 27.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.31), residues: 807 helix: 2.74 (0.22), residues: 531 sheet: -0.59 (1.04), residues: 24 loop : -1.53 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 79 PHE 0.010 0.001 PHE H 67 TYR 0.017 0.002 TYR D 80 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 772) hydrogen bonds : angle 3.19310 ( 1947) covalent geometry : bond 0.00411 (13293) covalent geometry : angle 0.56286 (19199) *********************** 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 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8919 (tpt90) cc_final: 0.8433 (tpt170) REVERT: B 35 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8173 (mtm180) REVERT: C 56 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8420 (tt0) REVERT: C 64 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8604 (tm-30) REVERT: C 99 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6605 (mtp85) REVERT: D 81 ASN cc_start: 0.8068 (t0) cc_final: 0.7720 (t0) REVERT: E 64 LYS cc_start: 0.7959 (mttt) cc_final: 0.7693 (tmtt) REVERT: G 64 GLU cc_start: 0.8138 (tt0) cc_final: 0.7890 (tm-30) REVERT: H 31 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7218 (pttp) REVERT: H 48 ASP cc_start: 0.9122 (p0) cc_final: 0.8822 (p0) REVERT: K 1 MET cc_start: 0.5050 (tmm) cc_final: 0.2048 (pmm) outliers start: 30 outliers final: 19 residues processed: 157 average time/residue: 0.2823 time to fit residues: 60.5914 Evaluate side-chains 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE 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 100 LEU Chi-restraints excluded: chain E residue 118 THR 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 86 ILE Chi-restraints excluded: chain H residue 120 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.099401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.067143 restraints weight = 33510.160| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.70 r_work: 0.2855 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13293 Z= 0.161 Angle : 0.554 7.488 19199 Z= 0.330 Chirality : 0.033 0.147 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.777 178.205 4085 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.90 % Allowed : 26.45 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.31), residues: 807 helix: 2.79 (0.22), residues: 532 sheet: -0.71 (1.01), residues: 24 loop : -1.45 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE H 67 TYR 0.014 0.001 TYR D 80 ARG 0.003 0.000 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 772) hydrogen bonds : angle 3.10071 ( 1947) covalent geometry : bond 0.00347 (13293) covalent geometry : angle 0.55355 (19199) *********************** 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 162 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8954 (tpt90) cc_final: 0.8411 (tpt170) REVERT: B 35 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.8197 (mtm180) REVERT: B 53 GLU cc_start: 0.8472 (mp0) cc_final: 0.8168 (mp0) REVERT: C 56 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8388 (tt0) REVERT: C 64 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8590 (tm-30) REVERT: C 99 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6730 (mtp85) REVERT: D 81 ASN cc_start: 0.7982 (t0) cc_final: 0.7638 (t0) REVERT: G 64 GLU cc_start: 0.8105 (tt0) cc_final: 0.7885 (tm-30) REVERT: H 31 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7229 (pttp) REVERT: H 48 ASP cc_start: 0.9092 (p0) cc_final: 0.8784 (p0) REVERT: K 1 MET cc_start: 0.5021 (tmm) cc_final: 0.2131 (pmm) outliers start: 27 outliers final: 20 residues processed: 156 average time/residue: 0.2858 time to fit residues: 61.1090 Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 46 VAL 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 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 59 TYR 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 67 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.066551 restraints weight = 33080.975| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.67 r_work: 0.2838 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1782 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= 0.175 Angle : 0.571 9.257 19199 Z= 0.337 Chirality : 0.033 0.150 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.778 179.159 4085 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.19 % Allowed : 26.59 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.31), residues: 807 helix: 2.76 (0.22), residues: 533 sheet: -0.59 (1.02), residues: 24 loop : -1.43 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE H 67 TYR 0.019 0.002 TYR D 80 ARG 0.003 0.000 ARG K 42 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 772) hydrogen bonds : angle 3.20097 ( 1947) covalent geometry : bond 0.00385 (13293) covalent geometry : angle 0.57098 (19199) *********************** 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 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8971 (tpt90) cc_final: 0.8430 (tpt170) REVERT: B 35 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8217 (mtm180) REVERT: B 95 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8147 (ptp90) REVERT: C 56 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8398 (tt0) REVERT: C 64 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 99 ARG cc_start: 0.7590 (mtt180) cc_final: 0.6670 (mtp85) REVERT: D 81 ASN cc_start: 0.8017 (t0) cc_final: 0.7683 (t0) REVERT: E 125 GLN cc_start: 0.8644 (mt0) cc_final: 0.8418 (mt0) REVERT: G 64 GLU cc_start: 0.8150 (tt0) cc_final: 0.7923 (tm-30) REVERT: H 31 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7235 (pttp) REVERT: H 48 ASP cc_start: 0.9101 (p0) cc_final: 0.8786 (p0) REVERT: K 1 MET cc_start: 0.5233 (tmm) cc_final: 0.2185 (pmm) outliers start: 29 outliers final: 21 residues processed: 160 average time/residue: 0.2856 time to fit residues: 62.3215 Evaluate side-chains 156 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 95 ARG 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 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 80 TYR 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 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR 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 59 TYR 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 50 optimal weight: 0.8980 chunk 43 optimal weight: 0.0170 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.0070 chunk 85 optimal weight: 10.0000 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3741 r_free = 0.3741 target = 0.101268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069242 restraints weight = 33230.664| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.71 r_work: 0.2907 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13293 Z= 0.151 Angle : 0.557 9.479 19199 Z= 0.330 Chirality : 0.033 0.144 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.728 179.472 4085 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.18 % Allowed : 27.60 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.31), residues: 807 helix: 2.74 (0.22), residues: 535 sheet: -0.40 (1.04), residues: 24 loop : -1.25 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE H 67 TYR 0.016 0.001 TYR H 80 ARG 0.002 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 772) hydrogen bonds : angle 3.09352 ( 1947) covalent geometry : bond 0.00319 (13293) covalent geometry : angle 0.55738 (19199) *********************** 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 164 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8698 (mm-30) REVERT: A 129 ARG cc_start: 0.8990 (tpt90) cc_final: 0.8441 (tpt170) REVERT: B 35 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8151 (mtm180) REVERT: B 95 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8110 (ptp90) REVERT: C 56 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8376 (tt0) REVERT: C 64 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8567 (tm-30) REVERT: C 99 ARG cc_start: 0.7513 (mtt180) cc_final: 0.6524 (mtp85) REVERT: D 81 ASN cc_start: 0.7800 (t0) cc_final: 0.7476 (t0) REVERT: H 31 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7096 (ptpp) REVERT: H 48 ASP cc_start: 0.9075 (p0) cc_final: 0.8793 (p0) REVERT: H 81 ASN cc_start: 0.8283 (t0) cc_final: 0.8029 (t0) REVERT: K 1 MET cc_start: 0.5069 (tmm) cc_final: 0.2036 (pmm) outliers start: 22 outliers final: 15 residues processed: 159 average time/residue: 0.2748 time to fit residues: 59.6705 Evaluate side-chains 150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 95 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL 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 100 LEU Chi-restraints excluded: chain E residue 118 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.097445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064988 restraints weight = 32752.344| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.64 r_work: 0.2797 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13293 Z= 0.227 Angle : 0.640 9.576 19199 Z= 0.369 Chirality : 0.036 0.185 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.800 178.900 4085 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 27.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.31), residues: 807 helix: 2.54 (0.23), residues: 535 sheet: 0.94 (1.62), residues: 10 loop : -1.59 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.010 0.001 PHE B 61 TYR 0.031 0.002 TYR D 80 ARG 0.002 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.06375 ( 772) hydrogen bonds : angle 3.43556 ( 1947) covalent geometry : bond 0.00519 (13293) covalent geometry : angle 0.64050 (19199) *********************** 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 159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.9013 (tpt90) cc_final: 0.8459 (tpt170) REVERT: B 35 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8236 (mtm180) REVERT: C 56 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8453 (tt0) REVERT: C 64 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8622 (tm-30) REVERT: C 99 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6582 (mtp85) REVERT: D 81 ASN cc_start: 0.8167 (t0) cc_final: 0.7856 (t0) REVERT: E 64 LYS cc_start: 0.8042 (mttt) cc_final: 0.7804 (tmtt) REVERT: F 91 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8823 (ttpt) REVERT: H 31 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7234 (pttp) REVERT: H 48 ASP cc_start: 0.9131 (p0) cc_final: 0.8827 (p0) REVERT: H 82 LYS cc_start: 0.9289 (tptp) cc_final: 0.9064 (tptp) REVERT: H 102 GLU cc_start: 0.7052 (pm20) cc_final: 0.6800 (pm20) REVERT: K 1 MET cc_start: 0.5357 (tmm) cc_final: 0.2313 (pmm) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.2908 time to fit residues: 61.2516 Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE 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 D residue 120 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 91 LYS 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 86 ILE Chi-restraints excluded: chain H residue 120 SER 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 57 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 95 optimal weight: 7.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.099540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067251 restraints weight = 32788.418| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.68 r_work: 0.2856 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13293 Z= 0.168 Angle : 0.599 9.926 19199 Z= 0.348 Chirality : 0.034 0.181 2194 Planarity : 0.004 0.045 1427 Dihedral : 29.769 179.916 4085 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.75 % Allowed : 28.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.31), residues: 807 helix: 2.72 (0.23), residues: 532 sheet: -0.72 (1.01), residues: 24 loop : -1.50 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.010 0.001 PHE H 67 TYR 0.020 0.001 TYR D 80 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04995 ( 772) hydrogen bonds : angle 3.31476 ( 1947) covalent geometry : bond 0.00365 (13293) covalent geometry : angle 0.59925 (19199) ********************** 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 155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.9006 (tpt90) cc_final: 0.8466 (tpt170) REVERT: B 35 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8210 (mtm180) REVERT: C 56 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8451 (tt0) REVERT: C 64 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 99 ARG cc_start: 0.7474 (mtt180) cc_final: 0.6616 (mtp85) REVERT: D 59 MET cc_start: 0.9119 (tpp) cc_final: 0.8882 (mmm) REVERT: D 81 ASN cc_start: 0.8030 (t0) cc_final: 0.7691 (t0) REVERT: G 64 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8185 (tt0) REVERT: G 95 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8078 (tmmt) REVERT: H 31 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7198 (ptpp) REVERT: H 48 ASP cc_start: 0.9114 (p0) cc_final: 0.8859 (p0) REVERT: H 81 ASN cc_start: 0.8560 (t0) cc_final: 0.7966 (t0) REVERT: K 1 MET cc_start: 0.5328 (tmm) cc_final: 0.2286 (pmm) REVERT: K 15 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8527 (mm) outliers start: 19 outliers final: 15 residues processed: 150 average time/residue: 0.2726 time to fit residues: 56.3470 Evaluate side-chains 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 120 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 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 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 87 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 0.0060 chunk 96 optimal weight: 6.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.101049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068712 restraints weight = 32819.598| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.69 r_work: 0.2899 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13293 Z= 0.155 Angle : 0.584 9.328 19199 Z= 0.341 Chirality : 0.033 0.148 2194 Planarity : 0.004 0.045 1427 Dihedral : 29.730 178.632 4085 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.46 % Allowed : 28.18 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.31), residues: 807 helix: 2.73 (0.23), residues: 532 sheet: -0.45 (1.05), residues: 24 loop : -1.41 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE H 67 TYR 0.036 0.001 TYR F 88 ARG 0.002 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 772) hydrogen bonds : angle 3.24363 ( 1947) covalent geometry : bond 0.00333 (13293) covalent geometry : angle 0.58449 (19199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5408.31 seconds wall clock time: 94 minutes 10.15 seconds (5650.15 seconds total)