Starting phenix.real_space_refine on Sat Nov 16 23:28:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/11_2024/8g6q_29778_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/11_2024/8g6q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/11_2024/8g6q_29778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/11_2024/8g6q_29778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/11_2024/8g6q_29778_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6q_29778/11_2024/8g6q_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-5513/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: 7.13, per 1000 atoms: 0.57 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: 2.98 Conformation dependent library (CDL) restraints added in 978.6 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: 5.97 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: 4.81 Time building geometry restraints manager: 3.50 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: 1.190 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.050 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- 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= 0.188 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 *********************** 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 : 1.120 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: 0.3056 time to fit residues: 65.4315 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 : 0.987 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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= 0.381 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 *********************** 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 : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7337 (pp) REVERT: A 129 ARG cc_start: 0.8567 (tpt90) cc_final: 0.8211 (tpt170) REVERT: B 35 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7747 (ttp-170) REVERT: B 91 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8704 (ttmt) REVERT: C 56 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8154 (tt0) REVERT: C 64 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 99 ARG cc_start: 0.7225 (mtt180) cc_final: 0.6048 (mtp85) REVERT: E 64 LYS cc_start: 0.8164 (mttt) cc_final: 0.7768 (tmtt) REVERT: K 1 MET cc_start: 0.5097 (tmm) cc_final: 0.4221 (ppp) REVERT: K 15 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8617 (mm) outliers start: 19 outliers final: 12 residues processed: 143 average time/residue: 0.2912 time to fit residues: 56.8662 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 : 0.991 ------------------------------------------------------------------------------- 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 53 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13293 Z= 0.335 Angle : 0.608 6.009 19199 Z= 0.360 Chirality : 0.036 0.163 2194 Planarity : 0.005 0.048 1427 Dihedral : 29.948 175.515 4085 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.48 % Allowed : 26.01 % 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: 1.61 (0.30), residues: 807 helix: 2.35 (0.22), residues: 531 sheet: -0.85 (1.04), residues: 24 loop : -1.67 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.010 0.002 PHE H 67 TYR 0.013 0.002 TYR E 41 ARG 0.004 0.000 ARG B 35 *********************** 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 157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8672 (tpt90) cc_final: 0.8467 (tpt90) REVERT: B 35 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7779 (ttp-170) REVERT: C 56 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8239 (tt0) REVERT: C 64 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8369 (tm-30) REVERT: C 99 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6195 (mtp85) REVERT: D 43 LYS cc_start: 0.9012 (tppt) cc_final: 0.8798 (tppt) REVERT: D 81 ASN cc_start: 0.7939 (t0) cc_final: 0.7725 (t0) REVERT: E 64 LYS cc_start: 0.8098 (mttt) cc_final: 0.7699 (tmtt) REVERT: H 31 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7007 (ptpp) REVERT: H 82 LYS cc_start: 0.9340 (tptp) cc_final: 0.8997 (tptp) REVERT: K 1 MET cc_start: 0.5408 (tmm) cc_final: 0.2646 (pmm) outliers start: 31 outliers final: 22 residues processed: 153 average time/residue: 0.2826 time to fit residues: 59.3857 Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 D residue 38 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 F residue 70 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 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 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1702 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= 0.220 Angle : 0.562 6.787 19199 Z= 0.336 Chirality : 0.033 0.147 2194 Planarity : 0.004 0.048 1427 Dihedral : 29.870 176.590 4085 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.47 % Allowed : 27.17 % 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: 1.94 (0.30), residues: 807 helix: 2.65 (0.22), residues: 532 sheet: -0.82 (1.02), residues: 24 loop : -1.67 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.012 0.001 PHE H 67 TYR 0.011 0.001 TYR D 37 ARG 0.003 0.000 ARG B 35 *********************** 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: 24 poor density : 135 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8715 (tpt90) cc_final: 0.8439 (tpt90) REVERT: B 35 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7853 (mtm180) REVERT: C 56 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8193 (tt0) REVERT: C 64 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 99 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6266 (mtp85) REVERT: D 43 LYS cc_start: 0.9010 (tppt) cc_final: 0.8787 (tppt) REVERT: D 81 ASN cc_start: 0.7766 (t0) cc_final: 0.7487 (t0) REVERT: E 60 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7759 (mt) REVERT: G 64 GLU cc_start: 0.7903 (tt0) cc_final: 0.7601 (tm-30) REVERT: H 31 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7022 (pttp) REVERT: H 82 LYS cc_start: 0.9305 (tptp) cc_final: 0.8990 (tptp) REVERT: K 1 MET cc_start: 0.5192 (tmm) cc_final: 0.2249 (pmm) REVERT: K 15 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8647 (mm) REVERT: K 68 HIS cc_start: 0.8774 (t70) cc_final: 0.8503 (t70) outliers start: 24 outliers final: 13 residues processed: 156 average time/residue: 0.2920 time to fit residues: 62.2092 Evaluate side-chains 144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain E residue 60 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN ** G 38 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13293 Z= 0.355 Angle : 0.624 6.499 19199 Z= 0.368 Chirality : 0.037 0.182 2194 Planarity : 0.005 0.049 1427 Dihedral : 29.923 177.417 4085 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.92 % Allowed : 25.58 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.30), residues: 807 helix: 2.42 (0.22), residues: 530 sheet: -1.04 (0.96), residues: 25 loop : -1.65 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.010 0.002 PHE H 67 TYR 0.013 0.002 TYR E 41 ARG 0.003 0.000 ARG B 35 *********************** 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 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8745 (tpt90) cc_final: 0.8459 (tpt90) REVERT: B 35 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7836 (mtm180) REVERT: C 56 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8278 (tt0) REVERT: C 64 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 99 ARG cc_start: 0.7273 (mtt180) cc_final: 0.6270 (mtp85) REVERT: D 43 LYS cc_start: 0.9029 (tppt) cc_final: 0.8799 (tppt) REVERT: D 81 ASN cc_start: 0.7996 (t0) cc_final: 0.7669 (t0) REVERT: E 64 LYS cc_start: 0.8116 (mttt) cc_final: 0.7717 (tmtt) REVERT: H 30 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7908 (mtt90) REVERT: H 31 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7017 (ptpp) REVERT: H 82 LYS cc_start: 0.9371 (tptp) cc_final: 0.9029 (tptp) REVERT: K 1 MET cc_start: 0.5547 (tmm) cc_final: 0.2795 (pmm) REVERT: K 68 HIS cc_start: 0.8872 (t70) cc_final: 0.8606 (t70) outliers start: 41 outliers final: 27 residues processed: 161 average time/residue: 0.2836 time to fit residues: 62.1318 Evaluate side-chains 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 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 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 SER 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 67 LEU 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 92 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.0270 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 53 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1819 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= 0.179 Angle : 0.561 8.292 19199 Z= 0.333 Chirality : 0.033 0.145 2194 Planarity : 0.004 0.047 1427 Dihedral : 29.831 177.288 4085 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.34 % Allowed : 26.73 % 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 (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: 2.14 (0.31), residues: 807 helix: 2.76 (0.22), residues: 534 sheet: -0.74 (1.02), residues: 24 loop : -1.53 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.013 0.001 PHE H 67 TYR 0.011 0.001 TYR D 37 ARG 0.003 0.000 ARG K 42 *********************** 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 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8736 (tpt90) cc_final: 0.8432 (tpt90) REVERT: B 35 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7864 (mtm180) REVERT: B 53 GLU cc_start: 0.8596 (mp0) cc_final: 0.8282 (mp0) REVERT: B 95 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7843 (ptp90) REVERT: C 56 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8146 (tt0) REVERT: C 64 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8334 (tm-30) REVERT: C 99 ARG cc_start: 0.7219 (mtt180) cc_final: 0.6395 (mtp-110) REVERT: D 43 LYS cc_start: 0.8995 (tppt) cc_final: 0.8792 (tppt) REVERT: D 81 ASN cc_start: 0.7599 (t0) cc_final: 0.7307 (t0) REVERT: G 64 GLU cc_start: 0.7819 (tt0) cc_final: 0.7584 (tm-30) REVERT: H 31 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.6987 (pttp) REVERT: H 82 LYS cc_start: 0.9241 (tptp) cc_final: 0.8953 (tptp) REVERT: K 1 MET cc_start: 0.5320 (tmm) cc_final: 0.2723 (pmm) outliers start: 30 outliers final: 18 residues processed: 164 average time/residue: 0.2968 time to fit residues: 66.2769 Evaluate side-chains 153 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 33 SER 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 G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER 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 11 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 GLN ** G 38 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1891 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= 0.214 Angle : 0.571 6.358 19199 Z= 0.339 Chirality : 0.034 0.160 2194 Planarity : 0.004 0.047 1427 Dihedral : 29.828 179.088 4085 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.76 % Allowed : 27.02 % 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: 2.11 (0.31), residues: 807 helix: 2.76 (0.22), residues: 532 sheet: 0.80 (1.65), residues: 10 loop : -1.60 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 75 PHE 0.012 0.001 PHE H 67 TYR 0.042 0.002 TYR D 80 ARG 0.007 0.000 ARG K 42 *********************** 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 160 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8742 (tpt90) cc_final: 0.8427 (tpt90) REVERT: B 35 ARG cc_start: 0.8151 (ttm-80) cc_final: 0.7893 (mtm180) REVERT: B 95 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7734 (ptp90) REVERT: C 56 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8208 (tt0) REVERT: C 64 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 99 ARG cc_start: 0.7286 (mtt180) cc_final: 0.6323 (mtp85) REVERT: D 43 LYS cc_start: 0.8991 (tppt) cc_final: 0.8747 (tppt) REVERT: D 59 MET cc_start: 0.8805 (tpp) cc_final: 0.8558 (mmm) REVERT: D 81 ASN cc_start: 0.7545 (t0) cc_final: 0.7282 (t0) REVERT: E 125 GLN cc_start: 0.8410 (mt0) cc_final: 0.8143 (mt0) REVERT: G 64 GLU cc_start: 0.7852 (tt0) cc_final: 0.7595 (tm-30) REVERT: H 30 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7896 (mtt90) REVERT: H 31 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7005 (pttp) REVERT: H 48 ASP cc_start: 0.9134 (p0) cc_final: 0.8916 (p0) REVERT: H 82 LYS cc_start: 0.9239 (tptp) cc_final: 0.8972 (tptp) REVERT: K 1 MET cc_start: 0.5365 (tmm) cc_final: 0.2770 (pmm) outliers start: 26 outliers final: 21 residues processed: 156 average time/residue: 0.2978 time to fit residues: 62.9828 Evaluate side-chains 155 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 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 33 SER 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 G residue 16 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 88 SER 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 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1922 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= 0.178 Angle : 0.557 6.465 19199 Z= 0.331 Chirality : 0.033 0.143 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.770 179.058 4085 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.76 % Allowed : 26.45 % 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: 2.22 (0.31), residues: 807 helix: 2.78 (0.22), residues: 534 sheet: -1.07 (1.00), residues: 24 loop : -1.31 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.012 0.001 PHE H 67 TYR 0.028 0.002 TYR D 80 ARG 0.006 0.000 ARG K 42 *********************** 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 159 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8543 (mm-30) REVERT: A 129 ARG cc_start: 0.8751 (tpt90) cc_final: 0.8431 (tpt90) REVERT: B 35 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7893 (mtm180) REVERT: B 95 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7833 (ptp90) REVERT: C 56 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8191 (tt0) REVERT: C 64 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 99 ARG cc_start: 0.7226 (mtt180) cc_final: 0.6311 (mtp85) REVERT: D 43 LYS cc_start: 0.8972 (tppt) cc_final: 0.8747 (tppt) REVERT: D 59 MET cc_start: 0.8787 (tpp) cc_final: 0.8563 (mmm) REVERT: D 81 ASN cc_start: 0.7413 (t0) cc_final: 0.7176 (t0) REVERT: D 98 LEU cc_start: 0.8226 (mp) cc_final: 0.7983 (mp) REVERT: G 64 GLU cc_start: 0.7815 (tt0) cc_final: 0.7601 (tm-30) REVERT: H 31 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.6932 (ptpp) REVERT: K 1 MET cc_start: 0.5575 (tmm) cc_final: 0.2886 (pmm) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.2897 time to fit residues: 61.5076 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 : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 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 33 SER 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 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 88 SER Chi-restraints excluded: chain H residue 120 SER 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 95 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.0670 chunk 100 optimal weight: 10.0000 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 13293 Z= 0.345 Angle : 0.639 6.969 19199 Z= 0.375 Chirality : 0.037 0.158 2194 Planarity : 0.005 0.046 1427 Dihedral : 29.851 179.067 4085 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.61 % Allowed : 27.02 % 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: 1.82 (0.31), residues: 807 helix: 2.52 (0.22), residues: 533 sheet: -1.04 (1.06), residues: 22 loop : -1.61 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.009 0.001 PHE B 61 TYR 0.040 0.002 TYR H 80 ARG 0.002 0.000 ARG D 76 *********************** 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 152 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8760 (tpt90) cc_final: 0.8433 (tpt90) REVERT: B 35 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7877 (mtm180) REVERT: B 84 MET cc_start: 0.7934 (mmm) cc_final: 0.7437 (tpt) REVERT: B 95 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7730 (ptp90) REVERT: C 56 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8287 (tt0) REVERT: C 64 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 99 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6215 (mtp85) REVERT: D 43 LYS cc_start: 0.9030 (tppt) cc_final: 0.8820 (tppt) REVERT: E 45 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 64 LYS cc_start: 0.8185 (mttt) cc_final: 0.7783 (tmtt) REVERT: G 64 GLU cc_start: 0.7957 (tt0) cc_final: 0.7628 (tm-30) REVERT: H 31 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7041 (pttp) REVERT: H 48 ASP cc_start: 0.9172 (p0) cc_final: 0.8956 (p0) REVERT: K 1 MET cc_start: 0.5738 (tmm) cc_final: 0.3185 (pmm) outliers start: 25 outliers final: 19 residues processed: 149 average time/residue: 0.3030 time to fit residues: 61.1434 Evaluate side-chains 145 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 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 120 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER 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 61 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13293 Z= 0.204 Angle : 0.594 6.857 19199 Z= 0.351 Chirality : 0.034 0.147 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.811 179.798 4085 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.32 % Allowed : 27.46 % 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: 2.06 (0.31), residues: 807 helix: 2.67 (0.22), residues: 535 sheet: -0.94 (1.08), residues: 22 loop : -1.48 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS B 75 PHE 0.012 0.001 PHE H 67 TYR 0.040 0.002 TYR D 80 ARG 0.002 0.000 ARG B 35 ********************** 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 156 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8789 (tpt90) cc_final: 0.8477 (tpt90) REVERT: B 35 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7835 (mtm180) REVERT: B 84 MET cc_start: 0.7557 (mmm) cc_final: 0.7349 (tpt) REVERT: B 95 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7794 (ptp90) REVERT: C 56 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8201 (tt0) REVERT: C 64 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8347 (tm-30) REVERT: C 99 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6243 (mtp85) REVERT: D 43 LYS cc_start: 0.8988 (tppt) cc_final: 0.8744 (tppt) REVERT: D 59 MET cc_start: 0.8806 (tpp) cc_final: 0.8600 (mmm) REVERT: D 90 GLU cc_start: 0.8151 (mp0) cc_final: 0.7916 (mp0) REVERT: G 64 GLU cc_start: 0.7889 (tt0) cc_final: 0.7604 (tm-30) REVERT: H 31 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.6960 (ptpp) REVERT: K 1 MET cc_start: 0.5613 (tmm) cc_final: 0.3098 (pmm) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.2831 time to fit residues: 58.9422 Evaluate side-chains 152 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 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 81 ASN 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 G residue 16 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 120 SER 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 25 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** K 31 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 = 0.3703 r_free = 0.3703 target = 0.098965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.067400 restraints weight = 32763.152| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.59 r_work: 0.2855 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13293 Z= 0.196 Angle : 0.588 6.904 19199 Z= 0.348 Chirality : 0.034 0.210 2194 Planarity : 0.004 0.046 1427 Dihedral : 29.792 179.157 4085 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.47 % Allowed : 27.31 % 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: 2.08 (0.31), residues: 807 helix: 2.68 (0.22), residues: 532 sheet: -1.06 (0.99), residues: 25 loop : -1.38 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 75 PHE 0.012 0.001 PHE H 67 TYR 0.017 0.001 TYR B 88 ARG 0.005 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.13 seconds wall clock time: 41 minutes 9.84 seconds (2469.84 seconds total)