Starting phenix.real_space_refine on Wed Mar 4 01:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7a_10391/03_2026/6t7a_10391.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7a_10391/03_2026/6t7a_10391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t7a_10391/03_2026/6t7a_10391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7a_10391/03_2026/6t7a_10391.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7a_10391/03_2026/6t7a_10391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7a_10391/03_2026/6t7a_10391.cif" } resolution = 3.7 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= 0.003 sd= 0.021 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 190 5.49 5 S 10 5.16 5 C 5889 2.51 5 N 1960 2.21 5 O 2289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1936 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "J" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1959 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 2, 'TRP:plan': 2, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 2.58, per 1000 atoms: 0.25 Number of scatterers: 10338 At special positions: 0 Unit cell: (85.05, 115.5, 129.15, 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 10 16.00 P 190 15.00 O 2289 8.00 N 1960 7.00 C 5889 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 385.1 milliseconds 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 68.2% alpha, 1.9% beta 93 base pairs and 171 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.965A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.511A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.534A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.769A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 4.227A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.160A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.810A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.184A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.540A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.585A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.331A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.722A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.046A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.809A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.185A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.540A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.584A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.331A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.602A pdb=" N VAL K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A 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 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: 7.264A 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 101 through 102 removed outlier: 7.451A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.507A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.375A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 408 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 171 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1653 1.33 - 1.44: 3477 1.44 - 1.56: 5364 1.56 - 1.68: 378 1.68 - 1.80: 20 Bond restraints: 10892 Sorted by residual: bond pdb=" C3' DT I 87 " pdb=" O3' DT I 87 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.32e+00 bond pdb=" C ILE K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.75e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.492 1.418 0.074 5.00e-02 4.00e+02 2.19e+00 bond pdb=" CA ILE F 26 " pdb=" C ILE F 26 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.27e-02 6.20e+03 2.11e+00 bond pdb=" CB ASN G 110 " pdb=" CG ASN G 110 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 14698 1.85 - 3.69: 692 3.69 - 5.54: 56 5.54 - 7.39: 12 7.39 - 9.23: 6 Bond angle restraints: 15464 Sorted by residual: angle pdb=" N ILE F 34 " pdb=" CA ILE F 34 " pdb=" C ILE F 34 " ideal model delta sigma weight residual 112.96 107.02 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " ideal model delta sigma weight residual 119.63 115.90 3.73 8.10e-01 1.52e+00 2.12e+01 angle pdb=" C ARG F 23 " pdb=" CA ARG F 23 " pdb=" CB ARG F 23 " ideal model delta sigma weight residual 116.63 111.29 5.34 1.16e+00 7.43e-01 2.12e+01 angle pdb=" C LYS K 88 " pdb=" N MET K 89 " pdb=" CA MET K 89 " ideal model delta sigma weight residual 122.54 115.16 7.38 1.65e+00 3.67e-01 2.00e+01 angle pdb=" CA LYS H 27 " pdb=" CB LYS H 27 " pdb=" CG LYS H 27 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 ... (remaining 15459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 4324 19.65 - 39.31: 919 39.31 - 58.96: 783 58.96 - 78.61: 52 78.61 - 98.26: 17 Dihedral angle restraints: 6095 sinusoidal: 3789 harmonic: 2306 Sorted by residual: dihedral pdb=" CA LYS D 27 " pdb=" C LYS D 27 " pdb=" N ARG D 28 " pdb=" CA ARG D 28 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LYS H 27 " pdb=" C LYS H 27 " pdb=" N ARG H 28 " pdb=" CA ARG H 28 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 6092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1240 0.048 - 0.096: 373 0.096 - 0.144: 85 0.144 - 0.191: 15 0.191 - 0.239: 2 Chirality restraints: 1715 Sorted by residual: chirality pdb=" CB THR C 59 " pdb=" CA THR C 59 " pdb=" OG1 THR C 59 " pdb=" CG2 THR C 59 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB THR G 59 " pdb=" CA THR G 59 " pdb=" OG1 THR G 59 " pdb=" CG2 THR G 59 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1712 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C ASP F 24 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 60 " 0.028 2.00e-02 2.50e+03 1.50e-02 5.64e+00 pdb=" N1 DT I 60 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT I 60 " -0.014 2.00e-02 2.50e+03 pdb=" O2 DT I 60 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 60 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 60 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 60 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 60 " -0.012 2.00e-02 2.50e+03 pdb=" C6 DT I 60 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO C 80 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 146 2.62 - 3.19: 7862 3.19 - 3.76: 18565 3.76 - 4.33: 24486 4.33 - 4.90: 35606 Nonbonded interactions: 86665 Sorted by model distance: nonbonded pdb=" CB GLU E 73 " pdb=" CG ASN F 25 " model vdw 2.044 2.936 nonbonded pdb=" CD GLU E 73 " pdb=" CG ASN F 25 " model vdw 2.167 2.800 nonbonded pdb=" OE1 GLU E 73 " pdb=" CB ASN F 25 " model vdw 2.167 3.440 nonbonded pdb=" CB HIS F 18 " pdb=" OP1 DT I 87 " model vdw 2.168 3.440 nonbonded pdb=" CG GLU E 73 " pdb=" OD1 ASN F 25 " model vdw 2.219 2.752 ... (remaining 86660 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 16 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.870 Find NCS groups from input model: 0.120 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.009 0.697 10893 Z= 0.727 Angle : 0.870 9.233 15464 Z= 0.526 Chirality : 0.048 0.239 1715 Planarity : 0.006 0.058 1327 Dihedral : 26.125 98.264 4657 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.81 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.23), residues: 829 helix: -1.95 (0.16), residues: 569 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 92 TYR 0.027 0.002 TYR F 98 PHE 0.009 0.002 PHE D 62 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00638 (10892) covalent geometry : angle 0.86996 (15464) hydrogen bonds : bond 0.11019 ( 624) hydrogen bonds : angle 4.77767 ( 1641) Misc. bond : bond 0.69718 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9019 (t80) cc_final: 0.8623 (t80) REVERT: B 59 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8236 (mtpt) REVERT: B 60 VAL cc_start: 0.9049 (m) cc_final: 0.8010 (p) REVERT: B 63 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 92 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7676 (ttp80) REVERT: C 73 ASN cc_start: 0.8815 (t0) cc_final: 0.8556 (t0) REVERT: C 84 GLN cc_start: 0.8744 (tp40) cc_final: 0.8352 (tp-100) REVERT: D 85 THR cc_start: 0.9519 (m) cc_final: 0.9088 (p) REVERT: E 86 SER cc_start: 0.8750 (m) cc_final: 0.8499 (m) REVERT: E 124 ILE cc_start: 0.9285 (mt) cc_final: 0.8917 (mp) REVERT: F 59 LYS cc_start: 0.8804 (tttm) cc_final: 0.8597 (tttm) REVERT: F 60 VAL cc_start: 0.9172 (p) cc_final: 0.8677 (m) REVERT: F 70 VAL cc_start: 0.9486 (t) cc_final: 0.8584 (t) REVERT: F 71 THR cc_start: 0.9269 (p) cc_final: 0.8683 (p) REVERT: G 56 GLU cc_start: 0.8181 (tt0) cc_final: 0.7931 (tt0) REVERT: G 71 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8617 (ttp80) REVERT: H 51 ILE cc_start: 0.8660 (tt) cc_final: 0.8417 (tt) REVERT: H 73 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7633 (mm-30) REVERT: H 80 TYR cc_start: 0.8678 (m-10) cc_final: 0.7979 (m-10) REVERT: H 85 THR cc_start: 0.9140 (m) cc_final: 0.8620 (p) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.1483 time to fit residues: 63.2733 Evaluate side-chains 232 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 89 ASN C 112 GLN D 92 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.077291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056321 restraints weight = 37891.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.058144 restraints weight = 18877.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.059373 restraints weight = 12442.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060141 restraints weight = 9697.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.060603 restraints weight = 8391.739| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10893 Z= 0.171 Angle : 0.633 7.454 15464 Z= 0.371 Chirality : 0.037 0.178 1715 Planarity : 0.005 0.033 1327 Dihedral : 29.134 87.541 3109 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.58 % Allowed : 16.49 % Favored : 79.94 % 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: -0.39 (0.27), residues: 829 helix: 0.20 (0.20), residues: 581 sheet: None (None), residues: 0 loop : -1.14 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 36 TYR 0.020 0.002 TYR E 99 PHE 0.006 0.001 PHE E 78 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00376 (10892) covalent geometry : angle 0.63275 (15464) hydrogen bonds : bond 0.04160 ( 624) hydrogen bonds : angle 3.33411 ( 1641) Misc. bond : bond 0.00255 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9287 (tt0) cc_final: 0.8869 (tm-30) REVERT: B 27 GLN cc_start: 0.8730 (mp10) cc_final: 0.8501 (mp10) REVERT: B 67 ARG cc_start: 0.9198 (ttm110) cc_final: 0.8815 (ttm110) REVERT: B 92 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7682 (ttp80) REVERT: C 64 GLU cc_start: 0.8503 (tt0) cc_final: 0.7769 (tm-30) REVERT: C 73 ASN cc_start: 0.9185 (t0) cc_final: 0.8842 (t0) REVERT: C 84 GLN cc_start: 0.8688 (tp40) cc_final: 0.8174 (tp40) REVERT: C 92 GLU cc_start: 0.8130 (pm20) cc_final: 0.7768 (pm20) REVERT: D 68 GLU cc_start: 0.9000 (tp30) cc_final: 0.8766 (tp30) REVERT: D 77 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8697 (mp) REVERT: D 83 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8142 (mmm-85) REVERT: D 90 GLU cc_start: 0.9230 (mp0) cc_final: 0.8659 (mp0) REVERT: E 86 SER cc_start: 0.8955 (m) cc_final: 0.8670 (p) REVERT: E 120 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7527 (mtt) REVERT: F 62 LEU cc_start: 0.9576 (mm) cc_final: 0.9341 (mm) REVERT: F 68 ASP cc_start: 0.9209 (m-30) cc_final: 0.8978 (m-30) REVERT: F 70 VAL cc_start: 0.9562 (t) cc_final: 0.8901 (m) REVERT: F 88 TYR cc_start: 0.8779 (m-10) cc_final: 0.8280 (m-10) REVERT: G 41 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8249 (mp0) REVERT: G 56 GLU cc_start: 0.8950 (tt0) cc_final: 0.8350 (tt0) REVERT: G 104 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: H 34 TYR cc_start: 0.9386 (m-80) cc_final: 0.9058 (m-10) REVERT: H 73 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7889 (mm-30) REVERT: H 85 THR cc_start: 0.9081 (m) cc_final: 0.8488 (p) REVERT: H 96 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8694 (mtp85) REVERT: H 117 LYS cc_start: 0.9397 (mtmt) cc_final: 0.9180 (mtpt) outliers start: 23 outliers final: 13 residues processed: 287 average time/residue: 0.1096 time to fit residues: 42.1581 Evaluate side-chains 256 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 90 optimal weight: 40.0000 chunk 62 optimal weight: 30.0000 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.074259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053117 restraints weight = 38278.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054908 restraints weight = 18875.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056113 restraints weight = 12437.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056844 restraints weight = 9714.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057277 restraints weight = 8450.268| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10893 Z= 0.202 Angle : 0.642 6.963 15464 Z= 0.374 Chirality : 0.037 0.150 1715 Planarity : 0.004 0.039 1327 Dihedral : 28.965 87.995 3109 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.67 % Allowed : 21.62 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.28), residues: 829 helix: 1.62 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.036 0.003 TYR F 98 PHE 0.009 0.001 PHE F 100 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00448 (10892) covalent geometry : angle 0.64153 (15464) hydrogen bonds : bond 0.04374 ( 624) hydrogen bonds : angle 3.17204 ( 1641) Misc. bond : bond 0.00143 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9284 (tt0) cc_final: 0.8875 (tm-30) REVERT: A 51 ILE cc_start: 0.9325 (mt) cc_final: 0.9052 (mm) REVERT: A 62 ILE cc_start: 0.9205 (pp) cc_final: 0.8988 (pp) REVERT: A 79 LYS cc_start: 0.8393 (tptt) cc_final: 0.8150 (tptt) REVERT: A 90 MET cc_start: 0.8874 (mmp) cc_final: 0.8633 (mmp) REVERT: A 94 GLU cc_start: 0.8797 (tp30) cc_final: 0.8294 (mm-30) REVERT: A 97 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 118 THR cc_start: 0.9470 (m) cc_final: 0.8647 (p) REVERT: A 120 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.6800 (mpp) REVERT: B 27 GLN cc_start: 0.8776 (mp10) cc_final: 0.8567 (mp10) REVERT: B 46 ILE cc_start: 0.8958 (mm) cc_final: 0.8735 (mm) REVERT: B 53 GLU cc_start: 0.9126 (tp30) cc_final: 0.8891 (tp30) REVERT: B 67 ARG cc_start: 0.9226 (ttm110) cc_final: 0.8972 (ttm110) REVERT: B 84 MET cc_start: 0.7017 (tpp) cc_final: 0.6046 (tpp) REVERT: B 92 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7931 (ttp80) REVERT: C 64 GLU cc_start: 0.8605 (tt0) cc_final: 0.8009 (tm-30) REVERT: C 73 ASN cc_start: 0.9162 (t0) cc_final: 0.8792 (t0) REVERT: C 84 GLN cc_start: 0.8436 (tp40) cc_final: 0.8026 (tp40) REVERT: C 92 GLU cc_start: 0.7960 (pm20) cc_final: 0.7635 (pm20) REVERT: C 104 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7717 (mm-40) REVERT: D 59 MET cc_start: 0.9379 (mpp) cc_final: 0.9160 (mmp) REVERT: D 68 GLU cc_start: 0.8947 (tp30) cc_final: 0.8737 (tp30) REVERT: D 77 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8680 (mp) REVERT: D 90 GLU cc_start: 0.9259 (mp0) cc_final: 0.8650 (mp0) REVERT: D 110 GLU cc_start: 0.9057 (tp30) cc_final: 0.8819 (tp30) REVERT: E 50 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8592 (mm-30) REVERT: E 56 LYS cc_start: 0.9357 (mtpp) cc_final: 0.9137 (mtmm) REVERT: E 86 SER cc_start: 0.9068 (m) cc_final: 0.8788 (p) REVERT: E 123 ASP cc_start: 0.8992 (m-30) cc_final: 0.8694 (m-30) REVERT: E 125 GLN cc_start: 0.9268 (mm-40) cc_final: 0.9042 (mm110) REVERT: F 53 GLU cc_start: 0.8436 (tt0) cc_final: 0.7997 (tt0) REVERT: F 60 VAL cc_start: 0.9534 (p) cc_final: 0.9057 (m) REVERT: F 63 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8344 (mt-10) REVERT: F 68 ASP cc_start: 0.9268 (m-30) cc_final: 0.9050 (m-30) REVERT: G 41 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8348 (mp0) REVERT: G 56 GLU cc_start: 0.8988 (tt0) cc_final: 0.8393 (tt0) REVERT: G 61 GLU cc_start: 0.8978 (tp30) cc_final: 0.8636 (tp30) REVERT: G 64 GLU cc_start: 0.8513 (tp30) cc_final: 0.8264 (tp30) REVERT: H 34 TYR cc_start: 0.9431 (m-80) cc_final: 0.9157 (m-10) REVERT: H 44 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8296 (tm-30) REVERT: H 54 LYS cc_start: 0.8837 (ptpt) cc_final: 0.8625 (ptmt) REVERT: H 73 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8229 (mm-30) REVERT: H 83 ARG cc_start: 0.8646 (tpp-160) cc_final: 0.8225 (tpp-160) REVERT: H 85 THR cc_start: 0.8941 (m) cc_final: 0.8492 (p) REVERT: H 110 GLU cc_start: 0.9237 (tp30) cc_final: 0.8872 (tp30) REVERT: H 117 LYS cc_start: 0.9477 (mtmt) cc_final: 0.9140 (mtmt) outliers start: 30 outliers final: 17 residues processed: 264 average time/residue: 0.1148 time to fit residues: 40.1917 Evaluate side-chains 254 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 92 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** 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 = 0.3606 r_free = 0.3606 target = 0.075703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054604 restraints weight = 37919.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056453 restraints weight = 18519.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.057681 restraints weight = 12115.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.058447 restraints weight = 9408.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.058834 restraints weight = 8142.233| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10893 Z= 0.154 Angle : 0.601 7.946 15464 Z= 0.353 Chirality : 0.036 0.158 1715 Planarity : 0.004 0.031 1327 Dihedral : 28.787 89.080 3109 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.11 % Allowed : 24.57 % Favored : 72.32 % 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: 1.72 (0.28), residues: 829 helix: 2.02 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -0.75 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.017 0.002 TYR F 98 PHE 0.010 0.001 PHE A 84 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00341 (10892) covalent geometry : angle 0.60146 (15464) hydrogen bonds : bond 0.03720 ( 624) hydrogen bonds : angle 2.97385 ( 1641) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9259 (tt0) cc_final: 0.8865 (tm-30) REVERT: A 51 ILE cc_start: 0.9308 (mt) cc_final: 0.8991 (mm) REVERT: A 54 TYR cc_start: 0.8695 (m-80) cc_final: 0.8409 (m-80) REVERT: A 68 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7987 (tp40) REVERT: A 90 MET cc_start: 0.8876 (mmp) cc_final: 0.8602 (mmp) REVERT: A 93 GLN cc_start: 0.9259 (tt0) cc_final: 0.9000 (tp40) REVERT: A 94 GLU cc_start: 0.8756 (tp30) cc_final: 0.8393 (mm-30) REVERT: A 97 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8014 (mt-10) REVERT: B 31 LYS cc_start: 0.9031 (tttt) cc_final: 0.8706 (ttmt) REVERT: B 46 ILE cc_start: 0.8983 (mm) cc_final: 0.8778 (mm) REVERT: B 53 GLU cc_start: 0.9061 (tp30) cc_final: 0.8814 (tp30) REVERT: B 92 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7879 (ttp80) REVERT: C 64 GLU cc_start: 0.8612 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 73 ASN cc_start: 0.9149 (t0) cc_final: 0.8786 (t0) REVERT: C 75 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8833 (tptp) REVERT: C 84 GLN cc_start: 0.8434 (tp40) cc_final: 0.8003 (tp40) REVERT: C 92 GLU cc_start: 0.7809 (pm20) cc_final: 0.7143 (pm20) REVERT: C 104 GLN cc_start: 0.8504 (mm-40) cc_final: 0.7658 (mm-40) REVERT: D 43 LYS cc_start: 0.9226 (ttmm) cc_final: 0.8988 (tppt) REVERT: D 68 GLU cc_start: 0.8932 (tp30) cc_final: 0.8637 (tp30) REVERT: D 90 GLU cc_start: 0.9217 (mp0) cc_final: 0.8600 (mp0) REVERT: D 105 LYS cc_start: 0.9293 (ptpp) cc_final: 0.8803 (ptpp) REVERT: D 110 GLU cc_start: 0.8996 (tp30) cc_final: 0.8712 (tp30) REVERT: E 50 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8504 (mm-30) REVERT: E 56 LYS cc_start: 0.9327 (mtpp) cc_final: 0.9079 (mtmm) REVERT: E 86 SER cc_start: 0.9023 (m) cc_final: 0.8806 (p) REVERT: E 94 GLU cc_start: 0.8788 (tp30) cc_final: 0.8543 (tp30) REVERT: E 123 ASP cc_start: 0.9087 (m-30) cc_final: 0.8854 (m-30) REVERT: F 53 GLU cc_start: 0.8392 (tt0) cc_final: 0.7999 (tt0) REVERT: F 60 VAL cc_start: 0.9498 (p) cc_final: 0.8958 (m) REVERT: F 63 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8296 (mt-10) REVERT: F 68 ASP cc_start: 0.9201 (m-30) cc_final: 0.8880 (m-30) REVERT: F 74 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8214 (mp0) REVERT: F 88 TYR cc_start: 0.8688 (m-10) cc_final: 0.7103 (m-10) REVERT: G 56 GLU cc_start: 0.8969 (tt0) cc_final: 0.8382 (tt0) REVERT: G 61 GLU cc_start: 0.8964 (tp30) cc_final: 0.8728 (tp30) REVERT: G 64 GLU cc_start: 0.8558 (tp30) cc_final: 0.8214 (tp30) REVERT: G 104 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: H 34 TYR cc_start: 0.9407 (m-80) cc_final: 0.9193 (m-10) REVERT: H 44 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8347 (tm-30) REVERT: H 73 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8094 (tp30) REVERT: H 85 THR cc_start: 0.8963 (m) cc_final: 0.8684 (p) REVERT: H 117 LYS cc_start: 0.9490 (mtmt) cc_final: 0.9244 (mtmt) outliers start: 20 outliers final: 12 residues processed: 267 average time/residue: 0.1087 time to fit residues: 38.9034 Evaluate side-chains 246 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 93 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.073858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.052490 restraints weight = 38493.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054287 restraints weight = 19237.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055449 restraints weight = 12757.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056198 restraints weight = 10006.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056643 restraints weight = 8697.193| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10893 Z= 0.198 Angle : 0.641 9.776 15464 Z= 0.369 Chirality : 0.037 0.159 1715 Planarity : 0.004 0.030 1327 Dihedral : 28.793 89.996 3109 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.58 % Allowed : 24.57 % Favored : 71.85 % 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: 2.14 (0.28), residues: 829 helix: 2.29 (0.21), residues: 562 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.042 0.002 TYR H 80 PHE 0.008 0.001 PHE E 78 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00445 (10892) covalent geometry : angle 0.64108 (15464) hydrogen bonds : bond 0.04310 ( 624) hydrogen bonds : angle 3.11853 ( 1641) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9304 (tt0) cc_final: 0.8921 (tp30) REVERT: A 68 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8140 (tp40) REVERT: A 90 MET cc_start: 0.8901 (mmp) cc_final: 0.8612 (mmp) REVERT: A 94 GLU cc_start: 0.8713 (tp30) cc_final: 0.8308 (mm-30) REVERT: A 97 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8003 (mt-10) REVERT: B 31 LYS cc_start: 0.9105 (tttt) cc_final: 0.8875 (ttmt) REVERT: B 46 ILE cc_start: 0.9017 (mm) cc_final: 0.8790 (mm) REVERT: B 53 GLU cc_start: 0.9139 (tp30) cc_final: 0.8883 (tp30) REVERT: B 67 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8948 (ttm110) REVERT: B 84 MET cc_start: 0.6685 (tpp) cc_final: 0.6244 (tpp) REVERT: B 92 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7972 (ttp80) REVERT: C 64 GLU cc_start: 0.8656 (tt0) cc_final: 0.7980 (tm-30) REVERT: C 73 ASN cc_start: 0.9158 (t0) cc_final: 0.8791 (t0) REVERT: C 84 GLN cc_start: 0.8494 (tp40) cc_final: 0.8087 (tp40) REVERT: C 104 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7614 (mm-40) REVERT: D 68 GLU cc_start: 0.8889 (tp30) cc_final: 0.8609 (tp30) REVERT: D 90 GLU cc_start: 0.9276 (mp0) cc_final: 0.8599 (mp0) REVERT: D 102 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8301 (mm-30) REVERT: D 105 LYS cc_start: 0.9204 (ptpp) cc_final: 0.8864 (ptpp) REVERT: D 110 GLU cc_start: 0.8987 (tp30) cc_final: 0.8702 (tp30) REVERT: E 50 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8473 (mm-30) REVERT: E 56 LYS cc_start: 0.9381 (mtpp) cc_final: 0.9124 (mtmm) REVERT: E 82 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8608 (mm) REVERT: E 94 GLU cc_start: 0.8832 (tp30) cc_final: 0.8576 (tp30) REVERT: E 123 ASP cc_start: 0.9027 (m-30) cc_final: 0.8760 (m-30) REVERT: F 60 VAL cc_start: 0.9500 (p) cc_final: 0.8883 (m) REVERT: F 63 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8344 (mt-10) REVERT: F 68 ASP cc_start: 0.9257 (m-30) cc_final: 0.8991 (m-30) REVERT: F 88 TYR cc_start: 0.8533 (m-10) cc_final: 0.8190 (m-10) REVERT: G 56 GLU cc_start: 0.9012 (tt0) cc_final: 0.8429 (tt0) REVERT: G 61 GLU cc_start: 0.8989 (tp30) cc_final: 0.8778 (tp30) REVERT: G 64 GLU cc_start: 0.8621 (tp30) cc_final: 0.8218 (tp30) REVERT: G 75 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8883 (mmtp) REVERT: G 95 LYS cc_start: 0.9416 (mtpp) cc_final: 0.9208 (mtpp) REVERT: H 34 TYR cc_start: 0.9441 (m-80) cc_final: 0.9239 (m-10) REVERT: H 44 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8578 (tm-30) REVERT: H 73 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7945 (tp30) REVERT: H 83 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8451 (tpp80) REVERT: H 85 THR cc_start: 0.8876 (m) cc_final: 0.8619 (p) REVERT: H 117 LYS cc_start: 0.9487 (mtmt) cc_final: 0.9225 (mtmt) outliers start: 23 outliers final: 17 residues processed: 252 average time/residue: 0.1128 time to fit residues: 38.2248 Evaluate side-chains 242 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.073139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.052017 restraints weight = 38175.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.053747 restraints weight = 19282.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054874 restraints weight = 12863.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055587 restraints weight = 10133.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056002 restraints weight = 8822.429| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10893 Z= 0.211 Angle : 0.647 7.256 15464 Z= 0.375 Chirality : 0.038 0.169 1715 Planarity : 0.004 0.039 1327 Dihedral : 28.800 89.131 3109 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.58 % Allowed : 26.28 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.28), residues: 829 helix: 2.35 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 72 TYR 0.029 0.002 TYR H 80 PHE 0.008 0.001 PHE E 78 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00474 (10892) covalent geometry : angle 0.64687 (15464) hydrogen bonds : bond 0.04334 ( 624) hydrogen bonds : angle 3.21121 ( 1641) Misc. bond : bond 0.00108 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8860 (mmp) cc_final: 0.8581 (mmp) REVERT: A 94 GLU cc_start: 0.8681 (tp30) cc_final: 0.8290 (mm-30) REVERT: A 97 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 122 LYS cc_start: 0.9096 (pttt) cc_final: 0.8838 (pttp) REVERT: B 20 LYS cc_start: 0.8544 (tppp) cc_final: 0.8273 (mmmm) REVERT: B 46 ILE cc_start: 0.9105 (mm) cc_final: 0.8897 (mm) REVERT: B 53 GLU cc_start: 0.9109 (tp30) cc_final: 0.8872 (tp30) REVERT: B 67 ARG cc_start: 0.9169 (ttm110) cc_final: 0.8893 (ttm110) REVERT: B 84 MET cc_start: 0.6928 (tpp) cc_final: 0.6299 (tpp) REVERT: B 92 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8069 (ttp80) REVERT: C 41 GLU cc_start: 0.8087 (mp0) cc_final: 0.7866 (mp0) REVERT: C 64 GLU cc_start: 0.8617 (tt0) cc_final: 0.8042 (tm-30) REVERT: C 73 ASN cc_start: 0.9032 (t0) cc_final: 0.8718 (t0) REVERT: C 84 GLN cc_start: 0.8574 (tp40) cc_final: 0.8136 (tp-100) REVERT: C 104 GLN cc_start: 0.8592 (mm-40) cc_final: 0.7659 (mm-40) REVERT: C 112 GLN cc_start: 0.8793 (mp10) cc_final: 0.8590 (mp10) REVERT: D 43 LYS cc_start: 0.9262 (ttmm) cc_final: 0.9023 (tppt) REVERT: D 68 GLU cc_start: 0.8844 (tp30) cc_final: 0.8617 (tp30) REVERT: D 90 GLU cc_start: 0.9259 (mp0) cc_final: 0.8583 (mp0) REVERT: D 110 GLU cc_start: 0.8883 (tp30) cc_final: 0.8623 (tp30) REVERT: D 117 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9029 (ttmt) REVERT: E 50 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8494 (mm-30) REVERT: E 56 LYS cc_start: 0.9390 (mtpp) cc_final: 0.9111 (mtmm) REVERT: E 79 LYS cc_start: 0.8980 (tttm) cc_final: 0.8686 (tttp) REVERT: E 82 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8346 (mm) REVERT: E 94 GLU cc_start: 0.8790 (tp30) cc_final: 0.8462 (tp30) REVERT: E 108 ASN cc_start: 0.9550 (t0) cc_final: 0.9332 (t0) REVERT: E 123 ASP cc_start: 0.9119 (m-30) cc_final: 0.8847 (m-30) REVERT: F 60 VAL cc_start: 0.9538 (p) cc_final: 0.8870 (m) REVERT: F 63 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8316 (mt-10) REVERT: F 68 ASP cc_start: 0.9168 (m-30) cc_final: 0.8917 (m-30) REVERT: F 88 TYR cc_start: 0.8650 (m-10) cc_final: 0.7804 (m-10) REVERT: G 56 GLU cc_start: 0.8977 (tt0) cc_final: 0.8432 (tt0) REVERT: G 64 GLU cc_start: 0.8645 (tp30) cc_final: 0.8082 (tp30) REVERT: H 37 TYR cc_start: 0.9138 (m-80) cc_final: 0.8933 (m-80) REVERT: H 44 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8621 (tm-30) REVERT: H 73 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7977 (tp30) REVERT: H 80 TYR cc_start: 0.8727 (m-10) cc_final: 0.8222 (m-80) REVERT: H 117 LYS cc_start: 0.9464 (mtmt) cc_final: 0.9210 (mtmt) outliers start: 23 outliers final: 17 residues processed: 254 average time/residue: 0.1127 time to fit residues: 38.1417 Evaluate side-chains 244 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 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 = 0.3559 r_free = 0.3559 target = 0.073153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052030 restraints weight = 37629.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053780 restraints weight = 18868.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054909 restraints weight = 12577.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.055630 restraints weight = 9919.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056027 restraints weight = 8638.000| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10893 Z= 0.199 Angle : 0.666 12.020 15464 Z= 0.381 Chirality : 0.038 0.205 1715 Planarity : 0.004 0.051 1327 Dihedral : 28.773 89.418 3109 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.42 % Allowed : 26.75 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.29), residues: 829 helix: 2.49 (0.21), residues: 559 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 76 TYR 0.028 0.002 TYR D 80 PHE 0.007 0.001 PHE F 100 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00452 (10892) covalent geometry : angle 0.66577 (15464) hydrogen bonds : bond 0.04224 ( 624) hydrogen bonds : angle 3.28315 ( 1641) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9348 (tp30) cc_final: 0.8947 (tp30) REVERT: A 90 MET cc_start: 0.8914 (mmp) cc_final: 0.8607 (mmp) REVERT: A 94 GLU cc_start: 0.8747 (tp30) cc_final: 0.8422 (mm-30) REVERT: A 97 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7971 (mt-10) REVERT: B 20 LYS cc_start: 0.8630 (tppp) cc_final: 0.8261 (mmmm) REVERT: B 46 ILE cc_start: 0.9038 (mm) cc_final: 0.8822 (mm) REVERT: B 53 GLU cc_start: 0.9171 (tp30) cc_final: 0.8919 (tp30) REVERT: B 67 ARG cc_start: 0.9195 (ttm110) cc_final: 0.8900 (ttm110) REVERT: B 92 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8070 (ttp80) REVERT: C 64 GLU cc_start: 0.8656 (tt0) cc_final: 0.7872 (tm-30) REVERT: C 73 ASN cc_start: 0.9110 (t0) cc_final: 0.8782 (t0) REVERT: C 84 GLN cc_start: 0.8515 (tp40) cc_final: 0.8054 (tp-100) REVERT: C 89 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8726 (m-40) REVERT: C 92 GLU cc_start: 0.7862 (pm20) cc_final: 0.7600 (pm20) REVERT: C 104 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7636 (mm-40) REVERT: D 43 LYS cc_start: 0.9257 (ttmm) cc_final: 0.9014 (tppt) REVERT: D 90 GLU cc_start: 0.9320 (mp0) cc_final: 0.8589 (mp0) REVERT: D 102 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8508 (mm-30) REVERT: D 105 LYS cc_start: 0.9219 (ptpp) cc_final: 0.8926 (ptpp) REVERT: D 110 GLU cc_start: 0.8926 (tp30) cc_final: 0.8639 (tp30) REVERT: D 117 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9034 (ttmt) REVERT: E 50 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 56 LYS cc_start: 0.9434 (mtpp) cc_final: 0.9111 (mtmm) REVERT: E 79 LYS cc_start: 0.8958 (tttm) cc_final: 0.8606 (tttp) REVERT: E 82 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8314 (mm) REVERT: E 94 GLU cc_start: 0.8862 (tp30) cc_final: 0.8525 (tp30) REVERT: E 123 ASP cc_start: 0.9117 (m-30) cc_final: 0.8855 (m-30) REVERT: F 60 VAL cc_start: 0.9513 (p) cc_final: 0.8852 (m) REVERT: F 63 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8345 (mt-10) REVERT: F 68 ASP cc_start: 0.9228 (m-30) cc_final: 0.8977 (m-30) REVERT: G 56 GLU cc_start: 0.9056 (tt0) cc_final: 0.8492 (tt0) REVERT: G 61 GLU cc_start: 0.9203 (tp30) cc_final: 0.8938 (tp30) REVERT: G 64 GLU cc_start: 0.8811 (tp30) cc_final: 0.8117 (tp30) REVERT: H 37 TYR cc_start: 0.9091 (m-80) cc_final: 0.8877 (m-80) REVERT: H 44 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8645 (tm-30) REVERT: H 73 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8041 (tp30) REVERT: H 80 TYR cc_start: 0.8711 (m-10) cc_final: 0.8272 (m-80) REVERT: H 117 LYS cc_start: 0.9472 (mtmt) cc_final: 0.9223 (mtmt) outliers start: 22 outliers final: 18 residues processed: 246 average time/residue: 0.1088 time to fit residues: 35.7588 Evaluate side-chains 237 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3559 r_free = 0.3559 target = 0.073173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052166 restraints weight = 38381.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053947 restraints weight = 19153.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055128 restraints weight = 12702.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.055845 restraints weight = 9924.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056275 restraints weight = 8625.140| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10893 Z= 0.192 Angle : 0.691 11.940 15464 Z= 0.390 Chirality : 0.038 0.168 1715 Planarity : 0.004 0.031 1327 Dihedral : 28.711 89.806 3109 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.27 % Allowed : 27.99 % Favored : 68.74 % 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: 2.34 (0.29), residues: 829 helix: 2.32 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -0.14 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.039 0.002 TYR D 80 PHE 0.006 0.001 PHE F 61 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00438 (10892) covalent geometry : angle 0.69124 (15464) hydrogen bonds : bond 0.04158 ( 624) hydrogen bonds : angle 3.31801 ( 1641) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9341 (tp30) cc_final: 0.9060 (tp30) REVERT: A 90 MET cc_start: 0.8890 (mmp) cc_final: 0.8587 (mmp) REVERT: A 94 GLU cc_start: 0.8762 (tp30) cc_final: 0.8448 (mm-30) REVERT: A 97 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8037 (mt-10) REVERT: A 120 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: B 20 LYS cc_start: 0.8746 (tppp) cc_final: 0.8340 (mmmm) REVERT: B 46 ILE cc_start: 0.9051 (mm) cc_final: 0.8834 (mm) REVERT: B 53 GLU cc_start: 0.9181 (tp30) cc_final: 0.8917 (tp30) REVERT: B 67 ARG cc_start: 0.9194 (ttm110) cc_final: 0.8889 (ttm110) REVERT: B 92 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8074 (ttp80) REVERT: C 64 GLU cc_start: 0.8660 (tt0) cc_final: 0.7852 (tm-30) REVERT: C 73 ASN cc_start: 0.9072 (t0) cc_final: 0.8736 (t0) REVERT: C 84 GLN cc_start: 0.8498 (tp40) cc_final: 0.8085 (tp-100) REVERT: C 104 GLN cc_start: 0.8543 (mm-40) cc_final: 0.7598 (mm-40) REVERT: D 43 LYS cc_start: 0.9242 (ttmm) cc_final: 0.9039 (tppt) REVERT: D 90 GLU cc_start: 0.9310 (mp0) cc_final: 0.8548 (mp0) REVERT: D 102 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8678 (mm-30) REVERT: D 105 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8978 (ptpp) REVERT: D 110 GLU cc_start: 0.8921 (tp30) cc_final: 0.8646 (tp30) REVERT: D 117 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9026 (ttmt) REVERT: E 50 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8585 (mm-30) REVERT: E 56 LYS cc_start: 0.9451 (mtpp) cc_final: 0.9097 (mtmm) REVERT: E 79 LYS cc_start: 0.8953 (tttm) cc_final: 0.8685 (tttp) REVERT: E 82 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8378 (mm) REVERT: E 94 GLU cc_start: 0.8846 (tp30) cc_final: 0.8516 (tp30) REVERT: E 123 ASP cc_start: 0.9140 (m-30) cc_final: 0.8923 (m-30) REVERT: F 64 ASN cc_start: 0.9285 (m-40) cc_final: 0.8976 (m110) REVERT: F 68 ASP cc_start: 0.9262 (m-30) cc_final: 0.9048 (m-30) REVERT: F 88 TYR cc_start: 0.8759 (m-10) cc_final: 0.8220 (m-10) REVERT: G 56 GLU cc_start: 0.9039 (tt0) cc_final: 0.8475 (tt0) REVERT: G 57 TYR cc_start: 0.9412 (t80) cc_final: 0.9096 (t80) REVERT: G 61 GLU cc_start: 0.9221 (tp30) cc_final: 0.8932 (tp30) REVERT: G 64 GLU cc_start: 0.8797 (tp30) cc_final: 0.8194 (tp30) REVERT: H 37 TYR cc_start: 0.9114 (m-80) cc_final: 0.8878 (m-80) REVERT: H 44 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8634 (tm-30) REVERT: H 96 ARG cc_start: 0.9113 (mtp85) cc_final: 0.8899 (mtp85) REVERT: H 117 LYS cc_start: 0.9466 (mtmt) cc_final: 0.9220 (mtmt) outliers start: 21 outliers final: 16 residues processed: 243 average time/residue: 0.1098 time to fit residues: 36.0449 Evaluate side-chains 237 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 0 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 89 ASN D 79 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.071983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.050733 restraints weight = 38752.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052457 restraints weight = 19563.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.053589 restraints weight = 13089.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054288 restraints weight = 10309.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.054694 restraints weight = 8981.514| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10893 Z= 0.227 Angle : 0.729 14.510 15464 Z= 0.407 Chirality : 0.039 0.205 1715 Planarity : 0.004 0.032 1327 Dihedral : 28.804 89.726 3109 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.58 % Allowed : 29.24 % Favored : 67.19 % 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: 2.40 (0.29), residues: 829 helix: 2.27 (0.21), residues: 577 sheet: None (None), residues: 0 loop : 0.02 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 99 TYR 0.056 0.002 TYR B 88 PHE 0.010 0.001 PHE F 100 HIS 0.017 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00518 (10892) covalent geometry : angle 0.72892 (15464) hydrogen bonds : bond 0.04591 ( 624) hydrogen bonds : angle 3.46343 ( 1641) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9366 (tp30) cc_final: 0.9056 (tp30) REVERT: A 90 MET cc_start: 0.8894 (mmp) cc_final: 0.8569 (mmp) REVERT: A 94 GLU cc_start: 0.8757 (tp30) cc_final: 0.8435 (mm-30) REVERT: A 97 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 20 LYS cc_start: 0.8728 (tppp) cc_final: 0.8255 (mmmm) REVERT: B 46 ILE cc_start: 0.9073 (mm) cc_final: 0.8868 (mm) REVERT: B 53 GLU cc_start: 0.9194 (tp30) cc_final: 0.8930 (tp30) REVERT: B 67 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8890 (ttm110) REVERT: B 92 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8131 (ttp80) REVERT: C 36 LYS cc_start: 0.9361 (mmmm) cc_final: 0.9007 (tptt) REVERT: C 64 GLU cc_start: 0.8665 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 73 ASN cc_start: 0.9058 (t0) cc_final: 0.8738 (t0) REVERT: C 84 GLN cc_start: 0.8532 (tp40) cc_final: 0.8057 (tp-100) REVERT: C 92 GLU cc_start: 0.7933 (pm20) cc_final: 0.7551 (pm20) REVERT: D 35 SER cc_start: 0.9305 (m) cc_final: 0.8908 (t) REVERT: D 56 MET cc_start: 0.8846 (tpp) cc_final: 0.8489 (tpp) REVERT: D 90 GLU cc_start: 0.9301 (mp0) cc_final: 0.8528 (mp0) REVERT: D 102 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8613 (mm-30) REVERT: D 110 GLU cc_start: 0.8942 (tp30) cc_final: 0.8676 (tp30) REVERT: D 117 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9052 (ttmt) REVERT: E 50 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8695 (mm-30) REVERT: E 56 LYS cc_start: 0.9475 (mtpp) cc_final: 0.9086 (mtmm) REVERT: E 79 LYS cc_start: 0.8932 (tttm) cc_final: 0.8679 (tttp) REVERT: E 82 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8455 (mm) REVERT: E 123 ASP cc_start: 0.9142 (m-30) cc_final: 0.8824 (m-30) REVERT: F 64 ASN cc_start: 0.9295 (m-40) cc_final: 0.8994 (m110) REVERT: G 56 GLU cc_start: 0.9018 (tt0) cc_final: 0.8454 (tt0) REVERT: G 61 GLU cc_start: 0.9208 (tp30) cc_final: 0.8942 (tp30) REVERT: G 64 GLU cc_start: 0.8841 (tp30) cc_final: 0.8197 (tp30) REVERT: G 75 LYS cc_start: 0.9172 (mmtp) cc_final: 0.8887 (mmtp) REVERT: H 44 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8646 (tm-30) REVERT: H 96 ARG cc_start: 0.9124 (mtp85) cc_final: 0.8907 (mtp85) REVERT: H 117 LYS cc_start: 0.9459 (mtmt) cc_final: 0.9169 (mtmt) outliers start: 23 outliers final: 19 residues processed: 238 average time/residue: 0.1032 time to fit residues: 33.4341 Evaluate side-chains 240 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 27 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 79 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.072583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051169 restraints weight = 38460.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052895 restraints weight = 19479.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054032 restraints weight = 13078.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054744 restraints weight = 10309.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055166 restraints weight = 8980.333| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 10893 Z= 0.203 Angle : 0.723 13.241 15464 Z= 0.405 Chirality : 0.039 0.188 1715 Planarity : 0.004 0.034 1327 Dihedral : 28.772 89.967 3109 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.42 % Allowed : 30.02 % Favored : 66.56 % 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: 2.39 (0.29), residues: 829 helix: 2.20 (0.21), residues: 583 sheet: None (None), residues: 0 loop : 0.11 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.070 0.003 TYR B 88 PHE 0.007 0.001 PHE F 100 HIS 0.016 0.002 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00466 (10892) covalent geometry : angle 0.72297 (15464) hydrogen bonds : bond 0.04338 ( 624) hydrogen bonds : angle 3.45308 ( 1641) Misc. bond : bond 0.00122 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9353 (tp30) cc_final: 0.9047 (tp30) REVERT: A 90 MET cc_start: 0.8890 (mmp) cc_final: 0.8575 (mmp) REVERT: A 94 GLU cc_start: 0.8745 (tp30) cc_final: 0.8448 (mm-30) REVERT: A 97 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 20 LYS cc_start: 0.8731 (tppp) cc_final: 0.8238 (mmmm) REVERT: B 46 ILE cc_start: 0.9076 (mm) cc_final: 0.8867 (mm) REVERT: B 53 GLU cc_start: 0.9177 (tp30) cc_final: 0.8913 (tp30) REVERT: B 67 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8888 (ttm110) REVERT: C 36 LYS cc_start: 0.9327 (mmmm) cc_final: 0.8979 (tptt) REVERT: C 64 GLU cc_start: 0.8661 (tt0) cc_final: 0.7915 (tm-30) REVERT: C 73 ASN cc_start: 0.9035 (t0) cc_final: 0.8727 (t0) REVERT: C 84 GLN cc_start: 0.8502 (tp40) cc_final: 0.8045 (tp-100) REVERT: C 104 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7752 (mm-40) REVERT: D 35 SER cc_start: 0.9314 (m) cc_final: 0.9068 (t) REVERT: D 90 GLU cc_start: 0.9303 (mp0) cc_final: 0.8532 (mp0) REVERT: D 110 GLU cc_start: 0.8942 (tp30) cc_final: 0.8654 (tp30) REVERT: D 117 LYS cc_start: 0.9496 (mmmt) cc_final: 0.9112 (ttmt) REVERT: E 50 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8694 (mm-30) REVERT: E 56 LYS cc_start: 0.9463 (mtpp) cc_final: 0.9067 (mtmm) REVERT: E 79 LYS cc_start: 0.8948 (tttm) cc_final: 0.8695 (tttp) REVERT: E 82 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8475 (mm) REVERT: E 123 ASP cc_start: 0.9157 (m-30) cc_final: 0.8867 (m-30) REVERT: G 56 GLU cc_start: 0.8996 (tt0) cc_final: 0.8428 (tt0) REVERT: G 57 TYR cc_start: 0.9433 (t80) cc_final: 0.9183 (t80) REVERT: G 61 GLU cc_start: 0.9217 (tp30) cc_final: 0.8932 (tp30) REVERT: G 64 GLU cc_start: 0.8841 (tp30) cc_final: 0.8254 (tp30) REVERT: G 75 LYS cc_start: 0.9191 (mmtp) cc_final: 0.8879 (mmtp) REVERT: H 44 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8621 (tm-30) REVERT: H 96 ARG cc_start: 0.9092 (mtp85) cc_final: 0.8884 (mtp85) REVERT: H 117 LYS cc_start: 0.9462 (mtmt) cc_final: 0.9193 (mtmt) outliers start: 22 outliers final: 18 residues processed: 242 average time/residue: 0.1001 time to fit residues: 33.3159 Evaluate side-chains 240 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 chunk 70 optimal weight: 5.9990 chunk 56 optimal weight: 0.0670 chunk 45 optimal weight: 0.0050 chunk 59 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 79 HIS D 106 HIS E 55 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 79 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.074985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.054301 restraints weight = 37789.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056083 restraints weight = 18682.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057281 restraints weight = 12287.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.058025 restraints weight = 9536.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058426 restraints weight = 8232.110| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10893 Z= 0.163 Angle : 0.731 14.488 15464 Z= 0.403 Chirality : 0.038 0.209 1715 Planarity : 0.004 0.031 1327 Dihedral : 28.609 89.411 3109 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.18 % Allowed : 31.42 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.29), residues: 829 helix: 2.17 (0.21), residues: 577 sheet: None (None), residues: 0 loop : 0.06 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.059 0.002 TYR B 88 PHE 0.008 0.001 PHE E 67 HIS 0.014 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00372 (10892) covalent geometry : angle 0.73139 (15464) hydrogen bonds : bond 0.03954 ( 624) hydrogen bonds : angle 3.38900 ( 1641) Misc. bond : bond 0.00096 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1671.57 seconds wall clock time: 29 minutes 30.36 seconds (1770.36 seconds total)