Starting phenix.real_space_refine on Fri Jul 3 05:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6q_29778/07_2026/8g6q_29778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6q_29778/07_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_29778/07_2026/8g6q_29778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6q_29778/07_2026/8g6q_29778_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g6q_29778/07_2026/8g6q_29778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6q_29778/07_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-dev-6108/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: 2.78, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 371.5 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: 1.75 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: 2.35 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 18399 1.96 - 3.91: 747 3.91 - 5.87: 47 5.87 - 7.83: 3 7.83 - 9.78: 3 Bond angle restraints: 19199 Sorted by residual: 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=" 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=" 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: 1.490 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.520 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: 16.660 ------------------------------------------------------------------------------- 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 : 0.758 9.784 19199 Z= 0.639 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 0.75762 / 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 : 0.339 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: 0.1451 time to fit residues: 31.3602 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 : 0.385 ------------------------------------------------------------------------------- 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 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 = 0.100073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067634 restraints weight = 33195.557| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.71 r_work: 0.2874 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 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 = 0.2877 r_free = 0.2877 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: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13293 Z= 0.163 Angle : 0.612 6.560 19199 Z= 0.370 Chirality : 0.042 0.220 2194 Planarity : 0.005 0.057 1427 Dihedral : 30.340 178.157 4085 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.73 % Allowed : 28.03 % Favored : 70.23 % 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: 2.15 (0.31), residues: 807 helix: 2.70 (0.23), residues: 530 sheet: -0.41 (1.10), residues: 24 loop : -1.29 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 35 TYR 0.010 0.001 TYR G 50 PHE 0.009 0.001 PHE H 67 HIS 0.015 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (13293) covalent geometry : angle 0.61184 / 0.37 (19199) hydrogen bonds : bond 0.05855 / 3.94 ( 772) hydrogen bonds : angle 3.34478 / 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 151 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8690 (tpt90) cc_final: 0.8340 (tpt170) REVERT: B 35 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8261 (ttp-170) REVERT: B 91 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8839 (ttmt) REVERT: C 64 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8619 (tm-30) REVERT: C 99 ARG cc_start: 0.7494 (mtt180) cc_final: 0.6355 (mtp85) REVERT: E 64 LYS cc_start: 0.7914 (mttt) cc_final: 0.7644 (tmtt) REVERT: G 64 GLU cc_start: 0.8119 (tt0) cc_final: 0.7886 (tm-30) REVERT: H 82 LYS cc_start: 0.9128 (tptp) cc_final: 0.8908 (tptp) REVERT: K 1 MET cc_start: 0.4489 (tmm) cc_final: 0.3229 (ppp) outliers start: 12 outliers final: 7 residues processed: 148 average time/residue: 0.1392 time to fit residues: 28.2477 Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.099826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067209 restraints weight = 33624.090| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.74 r_work: 0.2864 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2866 r_free = 0.2866 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 (19 function evaluations) r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1043 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= 0.158 Angle : 0.583 7.265 19199 Z= 0.354 Chirality : 0.041 0.222 2194 Planarity : 0.004 0.047 1427 Dihedral : 30.359 178.259 4085 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.75 % Allowed : 26.30 % Favored : 70.95 % 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: 2.09 (0.31), residues: 807 helix: 2.65 (0.22), residues: 533 sheet: -0.39 (1.13), residues: 24 loop : -1.39 (0.38), residues: 250 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 0.00273 / 0.16 (13293) covalent geometry : angle 0.58251 / 0.35 (19199) hydrogen bonds : bond 0.05680 / 3.78 ( 772) hydrogen bonds : angle 3.24178 / 2.33 ( 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 152 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8304 (tp40) cc_final: 0.8069 (tp-100) REVERT: A 129 ARG cc_start: 0.8758 (tpt90) cc_final: 0.8339 (tpt170) REVERT: B 35 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8221 (ttp-170) REVERT: C 64 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8645 (tm-30) REVERT: C 99 ARG cc_start: 0.7469 (mtt180) cc_final: 0.6371 (mtp85) REVERT: G 64 GLU cc_start: 0.8105 (tt0) cc_final: 0.7848 (tm-30) REVERT: H 48 ASP cc_start: 0.8986 (p0) cc_final: 0.8777 (p0) REVERT: H 82 LYS cc_start: 0.9194 (tptp) cc_final: 0.8938 (tptp) REVERT: K 1 MET cc_start: 0.4558 (tmm) cc_final: 0.3456 (ppp) REVERT: K 60 ASN cc_start: 0.8563 (m-40) cc_final: 0.8355 (m-40) REVERT: K 68 HIS cc_start: 0.8593 (t70) cc_final: 0.8357 (t70) outliers start: 19 outliers final: 10 residues processed: 148 average time/residue: 0.1230 time to fit residues: 25.0780 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.099589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066907 restraints weight = 33318.582| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.73 r_work: 0.2854 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 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 = 0.2856 r_free = 0.2856 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: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1254 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= 0.158 Angle : 0.581 7.206 19199 Z= 0.352 Chirality : 0.041 0.228 2194 Planarity : 0.004 0.048 1427 Dihedral : 30.356 178.739 4085 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.32 % Allowed : 26.73 % Favored : 69.94 % 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: -0.34 (1.13), residues: 24 loop : -1.46 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 42 TYR 0.009 0.001 TYR D 37 PHE 0.009 0.001 PHE H 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (13293) covalent geometry : angle 0.58088 / 0.35 (19199) hydrogen bonds : bond 0.05711 / 3.79 ( 772) hydrogen bonds : angle 3.23025 / 2.33 ( 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 159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7518 (pp) REVERT: A 76 GLN cc_start: 0.8285 (tp40) cc_final: 0.8049 (tp-100) REVERT: B 35 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8225 (ttp-170) REVERT: C 64 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8653 (tm-30) REVERT: C 99 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6445 (mtp85) REVERT: G 64 GLU cc_start: 0.8100 (tt0) cc_final: 0.7876 (tm-30) REVERT: H 31 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7129 (ptpp) REVERT: H 82 LYS cc_start: 0.9225 (tptp) cc_final: 0.8997 (tptp) REVERT: K 1 MET cc_start: 0.4834 (tmm) cc_final: 0.1679 (pmm) REVERT: K 24 GLU cc_start: 0.9636 (tp30) cc_final: 0.9113 (mp0) REVERT: K 60 ASN cc_start: 0.8514 (m-40) cc_final: 0.8286 (m-40) REVERT: K 68 HIS cc_start: 0.8574 (t70) cc_final: 0.8305 (t70) outliers start: 23 outliers final: 15 residues processed: 155 average time/residue: 0.1184 time to fit residues: 25.3523 Evaluate side-chains 144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 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 66 THR 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: 0.7980 chunk 19 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** K 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.098311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.065385 restraints weight = 33313.212| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.70 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 = 0.81 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 (9 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13293 Z= 0.181 Angle : 0.610 7.229 19199 Z= 0.363 Chirality : 0.042 0.234 2194 Planarity : 0.004 0.049 1427 Dihedral : 30.376 179.305 4085 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.19 % Allowed : 26.30 % 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 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: 2.62 (0.23), residues: 534 sheet: -0.39 (1.11), residues: 24 loop : -1.49 (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 H 67 HIS 0.013 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 (13293) covalent geometry : angle 0.60977 / 0.36 (19199) hydrogen bonds : bond 0.06306 / 4.19 ( 772) hydrogen bonds : angle 3.34619 / 2.41 ( 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: 29 poor density : 132 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7546 (pp) REVERT: A 76 GLN cc_start: 0.8344 (tp40) cc_final: 0.8125 (tp-100) REVERT: A 129 ARG cc_start: 0.8850 (tpt90) cc_final: 0.8643 (tpt170) REVERT: B 35 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8113 (ttp80) REVERT: C 64 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8645 (tm-30) REVERT: C 99 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6454 (mtp85) REVERT: D 103 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8470 (mp) REVERT: G 64 GLU cc_start: 0.8129 (tt0) cc_final: 0.7907 (tm-30) REVERT: H 31 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7224 (pttp) REVERT: H 48 ASP cc_start: 0.9108 (p0) cc_final: 0.8838 (p0) REVERT: H 82 LYS cc_start: 0.9274 (tptp) cc_final: 0.9044 (tptp) REVERT: K 1 MET cc_start: 0.5103 (tmm) cc_final: 0.2586 (pmm) REVERT: K 24 GLU cc_start: 0.9632 (tp30) cc_final: 0.9127 (mp0) REVERT: K 60 ASN cc_start: 0.8517 (m-40) cc_final: 0.8272 (m-40) outliers start: 29 outliers final: 21 residues processed: 157 average time/residue: 0.1149 time to fit residues: 24.9694 Evaluate side-chains 149 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 103 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.099106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.066465 restraints weight = 33005.444| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.69 r_work: 0.2845 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 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 = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1499 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= 0.156 Angle : 0.588 9.089 19199 Z= 0.354 Chirality : 0.041 0.239 2194 Planarity : 0.004 0.050 1427 Dihedral : 30.352 179.242 4085 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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 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: 2.10 (0.31), residues: 807 helix: 2.73 (0.23), residues: 531 sheet: -0.53 (1.08), residues: 24 loop : -1.51 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.011 0.001 TYR E 54 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 0.00272 / 0.16 (13293) covalent geometry : angle 0.58791 / 0.35 (19199) hydrogen bonds : bond 0.05710 / 3.78 ( 772) hydrogen bonds : angle 3.25643 / 2.34 ( 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 159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7587 (pp) REVERT: A 76 GLN cc_start: 0.8378 (tp40) cc_final: 0.8159 (tp-100) REVERT: B 35 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8074 (ttp80) REVERT: C 64 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 99 ARG cc_start: 0.7446 (mtt180) cc_final: 0.6493 (mtp-110) REVERT: G 64 GLU cc_start: 0.8117 (tt0) cc_final: 0.7909 (tm-30) REVERT: H 31 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7221 (pttp) REVERT: H 48 ASP cc_start: 0.9109 (p0) cc_final: 0.8850 (p0) REVERT: H 82 LYS cc_start: 0.9243 (tptp) cc_final: 0.9026 (tptp) REVERT: K 1 MET cc_start: 0.5067 (tmm) cc_final: 0.2413 (pmm) REVERT: K 24 GLU cc_start: 0.9606 (tp30) cc_final: 0.9094 (mp0) REVERT: K 60 ASN cc_start: 0.8537 (m-40) cc_final: 0.8281 (m-40) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.1314 time to fit residues: 28.1941 Evaluate side-chains 149 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 D residue 120 SER Chi-restraints excluded: chain E residue 46 VAL 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: 3.9990 chunk 77 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 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: 0.9990 chunk 40 optimal weight: 3.9990 chunk 85 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 64 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064783 restraints weight = 33376.137| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.70 r_work: 0.2805 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 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 = 0.2807 r_free = 0.2807 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: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13293 Z= 0.203 Angle : 0.640 8.528 19199 Z= 0.375 Chirality : 0.043 0.239 2194 Planarity : 0.004 0.051 1427 Dihedral : 30.388 179.826 4085 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.19 % Allowed : 26.88 % Favored : 68.93 % 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: 1.90 (0.31), residues: 807 helix: 2.61 (0.23), residues: 529 sheet: -0.16 (1.19), residues: 19 loop : -1.66 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 0.00414 / 0.20 (13293) covalent geometry : angle 0.64027 / 0.38 (19199) hydrogen bonds : bond 0.06543 / 4.34 ( 772) hydrogen bonds : angle 3.46423 / 2.49 ( 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 156 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8379 (tp40) cc_final: 0.8172 (tp-100) REVERT: A 129 ARG cc_start: 0.8833 (tpt90) cc_final: 0.8454 (tpt170) REVERT: B 35 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8231 (ttp80) REVERT: C 64 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 99 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6534 (mtp85) REVERT: D 81 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7636 (t0) REVERT: E 125 GLN cc_start: 0.8646 (mt0) cc_final: 0.8416 (mt0) REVERT: H 31 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7207 (pttm) REVERT: H 48 ASP cc_start: 0.9138 (p0) cc_final: 0.8887 (p0) REVERT: H 82 LYS cc_start: 0.9259 (tptp) cc_final: 0.9025 (tptp) REVERT: K 1 MET cc_start: 0.5212 (tmm) cc_final: 0.2586 (pmm) REVERT: K 24 GLU cc_start: 0.9617 (tp30) cc_final: 0.9122 (mp0) REVERT: K 60 ASN cc_start: 0.8597 (m-40) cc_final: 0.8373 (m-40) outliers start: 29 outliers final: 21 residues processed: 150 average time/residue: 0.1333 time to fit residues: 27.7945 Evaluate side-chains 147 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 81 ASN 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 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: 20.0000 chunk 97 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 30.0000 chunk 14 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.097118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064702 restraints weight = 32889.986| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.67 r_work: 0.2795 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 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 = 0.2796 r_free = 0.2796 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: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13293 Z= 0.215 Angle : 0.648 8.989 19199 Z= 0.380 Chirality : 0.044 0.243 2194 Planarity : 0.005 0.051 1427 Dihedral : 30.400 179.938 4085 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.76 % Allowed : 27.17 % 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: 1.77 (0.30), residues: 807 helix: 2.51 (0.22), residues: 530 sheet: -0.15 (1.18), residues: 19 loop : -1.75 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 42 TYR 0.014 0.002 TYR H 80 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 0.00451 / 0.22 (13293) covalent geometry : angle 0.64822 / 0.38 (19199) hydrogen bonds : bond 0.06744 / 4.46 ( 772) hydrogen bonds : angle 3.51819 / 2.53 ( 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 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8186 (mtm180) REVERT: C 64 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 99 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6637 (mtp85) REVERT: H 31 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7216 (pttm) REVERT: H 48 ASP cc_start: 0.9150 (p0) cc_final: 0.8904 (p0) REVERT: H 82 LYS cc_start: 0.9284 (tptp) cc_final: 0.9035 (tptp) REVERT: K 1 MET cc_start: 0.5282 (tmm) cc_final: 0.2638 (pmm) REVERT: K 24 GLU cc_start: 0.9607 (tp30) cc_final: 0.9143 (mp0) REVERT: K 60 ASN cc_start: 0.8628 (m-40) cc_final: 0.8377 (m-40) outliers start: 26 outliers final: 22 residues processed: 149 average time/residue: 0.1340 time to fit residues: 27.5949 Evaluate side-chains 149 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 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 15 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.5651 > 50: distance: 36 - 40: 17.831 distance: 40 - 41: 13.561 distance: 41 - 42: 15.337 distance: 42 - 43: 17.309 distance: 42 - 44: 7.252 distance: 44 - 45: 23.466 distance: 45 - 46: 9.370 distance: 46 - 47: 5.905 distance: 46 - 48: 37.358 distance: 48 - 49: 9.707 distance: 49 - 50: 5.347 distance: 49 - 52: 8.972 distance: 50 - 51: 10.363 distance: 50 - 55: 9.741 distance: 52 - 53: 16.563 distance: 52 - 54: 16.552 distance: 55 - 56: 12.689 distance: 56 - 57: 6.714 distance: 56 - 59: 11.977 distance: 57 - 58: 16.219 distance: 57 - 63: 10.701 distance: 59 - 60: 4.527 distance: 60 - 61: 13.526 distance: 60 - 62: 24.395 distance: 63 - 64: 7.845 distance: 63 - 69: 8.350 distance: 64 - 65: 5.660 distance: 64 - 67: 12.762 distance: 65 - 66: 8.691 distance: 65 - 70: 14.392 distance: 67 - 68: 12.034 distance: 68 - 69: 7.440 distance: 70 - 71: 7.107 distance: 71 - 72: 13.804 distance: 71 - 74: 10.727 distance: 72 - 73: 12.189 distance: 74 - 75: 17.626 distance: 75 - 76: 13.428 distance: 75 - 77: 12.345 distance: 79 - 80: 9.728 distance: 79 - 82: 6.995 distance: 80 - 81: 14.715 distance: 80 - 86: 12.433 distance: 82 - 83: 8.890 distance: 82 - 84: 18.801 distance: 83 - 85: 6.788 distance: 86 - 87: 11.188 distance: 87 - 88: 5.538 distance: 87 - 90: 17.331 distance: 88 - 89: 6.829 distance: 88 - 95: 12.341 distance: 90 - 91: 6.025 distance: 91 - 92: 16.001 distance: 92 - 93: 16.206 distance: 92 - 94: 12.682 distance: 95 - 96: 9.826 distance: 96 - 97: 19.779 distance: 96 - 99: 23.168 distance: 97 - 98: 8.866 distance: 97 - 101: 19.704 distance: 99 - 100: 12.616 distance: 101 - 102: 9.196 distance: 102 - 103: 7.550 distance: 102 - 105: 4.522 distance: 103 - 104: 20.018 distance: 103 - 108: 15.329 distance: 105 - 107: 12.822