Starting phenix.real_space_refine on Sun Jul 27 23:29:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7a_10391/07_2025/6t7a_10391.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7a_10391/07_2025/6t7a_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_10391/07_2025/6t7a_10391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7a_10391/07_2025/6t7a_10391.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7a_10391/07_2025/6t7a_10391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7a_10391/07_2025/6t7a_10391.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 16.12, per 1000 atoms: 1.56 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: 3.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 4.36 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: 4.23 Time building geometry restraints manager: 4.00 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: 2.400 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.090 Set scattering table: 0.190 Process input model: 42.750 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.006 0.001 HIS A 113 PHE 0.009 0.002 PHE D 62 TYR 0.027 0.002 TYR F 98 ARG 0.007 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.11019 ( 624) hydrogen bonds : angle 4.77767 ( 1641) covalent geometry : bond 0.00638 (10892) covalent geometry : angle 0.86996 (15464) 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 : 0.865 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: 0.9268 (p) cc_final: 0.8683 (p) REVERT: G 56 GLU cc_start: 0.8182 (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: 0.3591 time to fit residues: 152.8080 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 : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.0770 chunk 46 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.075734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054789 restraints weight = 38044.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056611 restraints weight = 18793.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057838 restraints weight = 12362.998| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10893 Z= 0.196 Angle : 0.649 7.305 15464 Z= 0.379 Chirality : 0.037 0.179 1715 Planarity : 0.005 0.034 1327 Dihedral : 29.166 87.308 3109 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.35 % Allowed : 15.86 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 829 helix: 0.32 (0.20), residues: 579 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.007 0.001 PHE F 100 TYR 0.022 0.002 TYR D 80 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 624) hydrogen bonds : angle 3.35450 ( 1641) covalent geometry : bond 0.00432 (10892) covalent geometry : angle 0.64925 (15464) Misc. bond : bond 0.00264 ( 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 300 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 1.121 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: 0.9357 (tt0) cc_final: 0.8905 (tm-30) REVERT: B 27 GLN cc_start: 0.8749 (mp10) cc_final: 0.8519 (mp10) REVERT: B 67 ARG cc_start: 0.9211 (ttm110) cc_final: 0.8840 (ttm110) REVERT: B 92 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7665 (ttp80) REVERT: C 36 LYS cc_start: 0.9486 (mmmt) cc_final: 0.8978 (mmmm) REVERT: C 64 GLU cc_start: 0.8541 (tt0) cc_final: 0.7938 (tm-30) REVERT: C 73 ASN cc_start: 0.9211 (t0) cc_final: 0.8836 (t0) REVERT: C 84 GLN cc_start: 0.8723 (tp40) cc_final: 0.8254 (tp40) REVERT: D 68 GLU cc_start: 0.9047 (tp30) cc_final: 0.8840 (tp30) REVERT: D 77 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8748 (mp) REVERT: D 83 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: D 90 GLU cc_start: 0.9297 (mp0) cc_final: 0.8681 (mp0) REVERT: E 86 SER cc_start: 0.9027 (m) cc_final: 0.8753 (p) REVERT: E 120 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7465 (mtt) REVERT: F 59 LYS cc_start: 0.9173 (tttm) cc_final: 0.8626 (tttm) REVERT: F 62 LEU cc_start: 0.9603 (mm) cc_final: 0.9385 (mm) REVERT: F 63 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8423 (mp0) REVERT: F 68 ASP cc_start: 0.9234 (m-30) cc_final: 0.9025 (m-30) REVERT: F 70 VAL cc_start: 0.9571 (t) cc_final: 0.8943 (m) REVERT: F 88 TYR cc_start: 0.8838 (m-10) cc_final: 0.8179 (m-10) REVERT: G 56 GLU cc_start: 0.8971 (tt0) cc_final: 0.8352 (tt0) REVERT: G 94 ASN cc_start: 0.9502 (t0) cc_final: 0.9283 (t0) REVERT: G 104 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: H 34 TYR cc_start: 0.9416 (m-80) cc_final: 0.9076 (m-10) REVERT: H 73 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7870 (mm-30) REVERT: H 85 THR cc_start: 0.9113 (m) cc_final: 0.8476 (p) REVERT: H 96 ARG cc_start: 0.9029 (mtp85) cc_final: 0.8811 (mtp85) REVERT: H 117 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9208 (mtmt) outliers start: 28 outliers final: 18 residues processed: 281 average time/residue: 0.4030 time to fit residues: 150.6436 Evaluate side-chains 260 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 239 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU 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 63 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL 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 14 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.074915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053972 restraints weight = 37841.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055763 restraints weight = 18887.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.056953 restraints weight = 12477.230| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10893 Z= 0.187 Angle : 0.620 6.890 15464 Z= 0.365 Chirality : 0.037 0.151 1715 Planarity : 0.004 0.030 1327 Dihedral : 28.986 87.921 3109 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 4.04 % Allowed : 20.84 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 829 helix: 1.57 (0.21), residues: 559 sheet: None (None), residues: 0 loop : -0.95 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.010 0.001 PHE A 84 TYR 0.032 0.002 TYR F 98 ARG 0.006 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 624) hydrogen bonds : angle 3.11911 ( 1641) covalent geometry : bond 0.00415 (10892) covalent geometry : angle 0.62049 (15464) Misc. bond : bond 0.00145 ( 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 275 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 0.969 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: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9278 (tt0) cc_final: 0.8883 (tm-30) REVERT: A 51 ILE cc_start: 0.9346 (mt) cc_final: 0.9080 (mm) REVERT: B 53 GLU cc_start: 0.9048 (tp30) cc_final: 0.8839 (tp30) REVERT: B 67 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8940 (ttm110) REVERT: B 92 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7940 (ttp80) REVERT: C 64 GLU cc_start: 0.8549 (tt0) cc_final: 0.8001 (tm-30) REVERT: C 73 ASN cc_start: 0.9165 (t0) cc_final: 0.8803 (t0) REVERT: C 84 GLN cc_start: 0.8630 (tp40) cc_final: 0.8197 (tp40) REVERT: C 92 GLU cc_start: 0.8016 (pm20) cc_final: 0.7552 (pm20) REVERT: C 104 GLN cc_start: 0.8596 (mm-40) cc_final: 0.7700 (mm-40) REVERT: D 39 TYR cc_start: 0.8896 (t80) cc_final: 0.8691 (t80) REVERT: D 77 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8775 (mp) REVERT: D 90 GLU cc_start: 0.9223 (mp0) cc_final: 0.8638 (mp0) REVERT: D 110 GLU cc_start: 0.9010 (tp30) cc_final: 0.8807 (tp30) REVERT: E 56 LYS cc_start: 0.9340 (mtpp) cc_final: 0.9072 (mtmm) REVERT: E 86 SER cc_start: 0.9037 (m) cc_final: 0.8777 (p) REVERT: E 123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8747 (m-30) REVERT: F 63 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8268 (mt-10) REVERT: F 68 ASP cc_start: 0.9196 (m-30) cc_final: 0.8963 (m-30) REVERT: F 88 TYR cc_start: 0.8738 (m-10) cc_final: 0.8364 (m-10) REVERT: G 56 GLU cc_start: 0.8960 (tt0) cc_final: 0.8382 (tt0) REVERT: G 64 GLU cc_start: 0.8464 (tp30) cc_final: 0.8255 (tp30) REVERT: H 34 TYR cc_start: 0.9390 (m-80) cc_final: 0.9108 (m-10) REVERT: H 54 LYS cc_start: 0.8783 (ptpt) cc_final: 0.8561 (ptmt) REVERT: H 73 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8255 (mm-30) REVERT: H 83 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.8092 (tpp-160) REVERT: H 85 THR cc_start: 0.8905 (m) cc_final: 0.8306 (p) REVERT: H 117 LYS cc_start: 0.9466 (mtmt) cc_final: 0.9132 (mtmt) outliers start: 26 outliers final: 18 residues processed: 259 average time/residue: 0.2767 time to fit residues: 94.8817 Evaluate side-chains 250 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 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 85 LEU 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 C residue 115 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain F residue 74 GLU 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 4 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN E 68 GLN E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.073192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.051636 restraints weight = 38983.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053333 restraints weight = 20551.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054435 restraints weight = 14103.061| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10893 Z= 0.229 Angle : 0.644 8.700 15464 Z= 0.376 Chirality : 0.038 0.156 1715 Planarity : 0.004 0.031 1327 Dihedral : 28.965 89.714 3109 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.82 % Allowed : 22.40 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.28), residues: 829 helix: 2.01 (0.21), residues: 561 sheet: None (None), residues: 0 loop : -0.77 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.009 0.001 PHE F 100 TYR 0.031 0.002 TYR B 88 ARG 0.006 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 624) hydrogen bonds : angle 3.19409 ( 1641) covalent geometry : bond 0.00507 (10892) covalent geometry : angle 0.64361 (15464) Misc. bond : bond 0.00115 ( 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 272 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 3.201 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: 0.9289 (tt0) cc_final: 0.8899 (tm-30) REVERT: A 51 ILE cc_start: 0.9391 (mt) cc_final: 0.9133 (mm) REVERT: B 53 GLU cc_start: 0.9115 (tp30) cc_final: 0.8890 (tp30) REVERT: B 67 ARG cc_start: 0.9166 (ttm110) cc_final: 0.8921 (ttm110) REVERT: B 84 MET cc_start: 0.6855 (tpp) cc_final: 0.6251 (tpp) REVERT: B 92 ARG cc_start: 0.8335 (ttp80) cc_final: 0.8042 (ttp80) REVERT: C 36 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9046 (mmmm) REVERT: C 64 GLU cc_start: 0.8622 (tt0) cc_final: 0.7983 (tm-30) REVERT: C 73 ASN cc_start: 0.9208 (t0) cc_final: 0.8838 (t0) REVERT: C 84 GLN cc_start: 0.8760 (tp40) cc_final: 0.8295 (tp40) REVERT: C 92 GLU cc_start: 0.7781 (pm20) cc_final: 0.7379 (pm20) REVERT: C 104 GLN cc_start: 0.8588 (mm-40) cc_final: 0.7764 (mm-40) REVERT: D 56 MET cc_start: 0.7829 (tpp) cc_final: 0.7531 (tpt) REVERT: D 90 GLU cc_start: 0.9182 (mp0) cc_final: 0.8628 (mp0) REVERT: D 110 GLU cc_start: 0.8937 (tp30) cc_final: 0.8697 (tp30) REVERT: D 117 LYS cc_start: 0.9468 (mmmt) cc_final: 0.9137 (mtpt) REVERT: E 56 LYS cc_start: 0.9367 (mtpp) cc_final: 0.9113 (mtmm) REVERT: E 86 SER cc_start: 0.9207 (m) cc_final: 0.8898 (p) REVERT: E 99 TYR cc_start: 0.9327 (t80) cc_final: 0.9126 (t80) REVERT: E 123 ASP cc_start: 0.8977 (m-30) cc_final: 0.8626 (m-30) REVERT: F 59 LYS cc_start: 0.9348 (tttm) cc_final: 0.8917 (tttm) REVERT: F 60 VAL cc_start: 0.9542 (p) cc_final: 0.8936 (m) REVERT: F 63 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8405 (mt-10) REVERT: F 68 ASP cc_start: 0.9147 (m-30) cc_final: 0.8941 (m-30) REVERT: F 88 TYR cc_start: 0.8825 (m-10) cc_final: 0.8026 (m-10) REVERT: G 56 GLU cc_start: 0.8961 (tt0) cc_final: 0.8397 (tt0) REVERT: G 64 GLU cc_start: 0.8565 (tp30) cc_final: 0.8231 (tp30) REVERT: G 75 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8957 (mmtp) REVERT: G 104 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8611 (pm20) REVERT: H 34 TYR cc_start: 0.9386 (m-80) cc_final: 0.9183 (m-10) REVERT: H 44 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8510 (tm-30) REVERT: H 73 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8041 (tp30) REVERT: H 83 ARG cc_start: 0.8681 (tpp-160) cc_final: 0.8476 (tpp80) REVERT: H 85 THR cc_start: 0.8976 (m) cc_final: 0.8566 (p) REVERT: H 117 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9159 (mtmt) outliers start: 31 outliers final: 23 residues processed: 255 average time/residue: 0.3339 time to fit residues: 114.8154 Evaluate side-chains 248 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU 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 C residue 116 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 74 GLU 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 104 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.071808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050798 restraints weight = 37884.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052535 restraints weight = 19138.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053667 restraints weight = 12763.382| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10893 Z= 0.240 Angle : 0.654 8.889 15464 Z= 0.380 Chirality : 0.038 0.159 1715 Planarity : 0.004 0.030 1327 Dihedral : 28.955 89.260 3109 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.20 % Allowed : 24.42 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.29), residues: 829 helix: 2.19 (0.21), residues: 561 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.009 0.001 PHE F 100 TYR 0.042 0.002 TYR D 80 ARG 0.005 0.000 ARG C 88 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 624) hydrogen bonds : angle 3.21735 ( 1641) covalent geometry : bond 0.00536 (10892) covalent geometry : angle 0.65444 (15464) Misc. bond : bond 0.00113 ( 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 258 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.908 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: 0.9330 (tt0) cc_final: 0.8901 (tm-30) REVERT: A 51 ILE cc_start: 0.9355 (mt) cc_final: 0.9072 (mm) REVERT: B 20 LYS cc_start: 0.8619 (tppt) cc_final: 0.8265 (mmmm) REVERT: B 53 GLU cc_start: 0.9232 (tp30) cc_final: 0.8982 (tp30) REVERT: B 67 ARG cc_start: 0.9228 (ttm110) cc_final: 0.8960 (ttm110) REVERT: B 84 MET cc_start: 0.7062 (tpp) cc_final: 0.6351 (tpp) REVERT: B 92 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8083 (ttp80) REVERT: C 36 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9012 (mmmm) REVERT: C 64 GLU cc_start: 0.8655 (tt0) cc_final: 0.7913 (tm-30) REVERT: C 73 ASN cc_start: 0.9137 (t0) cc_final: 0.8798 (t0) REVERT: C 84 GLN cc_start: 0.8618 (tp40) cc_final: 0.8241 (tp40) REVERT: C 104 GLN cc_start: 0.8688 (mm-40) cc_final: 0.7809 (mm-40) REVERT: D 90 GLU cc_start: 0.9280 (mp0) cc_final: 0.8578 (mp0) REVERT: D 110 GLU cc_start: 0.8969 (tp30) cc_final: 0.8702 (tp30) REVERT: D 117 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9074 (ttmt) REVERT: E 50 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8593 (mm-30) REVERT: E 56 LYS cc_start: 0.9396 (mtpp) cc_final: 0.9134 (mtmm) REVERT: E 94 GLU cc_start: 0.8785 (tp30) cc_final: 0.8542 (tp30) REVERT: E 123 ASP cc_start: 0.9146 (m-30) cc_final: 0.8832 (m-30) REVERT: F 63 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8330 (mt-10) REVERT: F 88 TYR cc_start: 0.8810 (m-10) cc_final: 0.8004 (m-10) REVERT: G 56 GLU cc_start: 0.9069 (tt0) cc_final: 0.8504 (tt0) REVERT: G 57 TYR cc_start: 0.9429 (t80) cc_final: 0.9114 (t80) REVERT: G 61 GLU cc_start: 0.9231 (tp30) cc_final: 0.8948 (tp30) REVERT: G 64 GLU cc_start: 0.8708 (tp30) cc_final: 0.8320 (tp30) REVERT: G 92 GLU cc_start: 0.8217 (pm20) cc_final: 0.7951 (pm20) REVERT: H 44 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8645 (tm-30) REVERT: H 73 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8217 (tp30) REVERT: H 85 THR cc_start: 0.8890 (m) cc_final: 0.8643 (p) REVERT: H 117 LYS cc_start: 0.9492 (mtmt) cc_final: 0.9225 (mtmt) outliers start: 27 outliers final: 20 residues processed: 243 average time/residue: 0.2614 time to fit residues: 84.7871 Evaluate side-chains 238 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 85 LEU 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 C residue 116 LEU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 74 GLU 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 59 THR Chi-restraints excluded: chain G residue 107 VAL 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 16 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** 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 = 0.3567 r_free = 0.3567 target = 0.073499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.052596 restraints weight = 37767.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.054416 restraints weight = 18777.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.055616 restraints weight = 12381.518| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10893 Z= 0.161 Angle : 0.616 9.725 15464 Z= 0.360 Chirality : 0.036 0.164 1715 Planarity : 0.003 0.028 1327 Dihedral : 28.782 89.892 3109 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.49 % Allowed : 27.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.29), residues: 829 helix: 2.35 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.55 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.010 0.001 PHE E 78 TYR 0.031 0.002 TYR D 80 ARG 0.005 0.000 ARG C 29 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 624) hydrogen bonds : angle 3.04916 ( 1641) covalent geometry : bond 0.00357 (10892) covalent geometry : angle 0.61605 (15464) Misc. bond : bond 0.00089 ( 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 259 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9325 (tt0) cc_final: 0.8936 (tm-30) REVERT: B 20 LYS cc_start: 0.8591 (tppt) cc_final: 0.8106 (mmmm) REVERT: B 53 GLU cc_start: 0.9187 (tp30) cc_final: 0.8926 (tp30) REVERT: B 92 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8017 (ttp80) REVERT: C 36 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9047 (mmmm) REVERT: C 64 GLU cc_start: 0.8630 (tt0) cc_final: 0.7780 (tm-30) REVERT: C 73 ASN cc_start: 0.9103 (t0) cc_final: 0.8775 (t0) REVERT: C 84 GLN cc_start: 0.8574 (tp40) cc_final: 0.8094 (tp40) REVERT: C 92 GLU cc_start: 0.7946 (pm20) cc_final: 0.7715 (pm20) REVERT: C 104 GLN cc_start: 0.8487 (mm-40) cc_final: 0.7670 (mm-40) REVERT: C 112 GLN cc_start: 0.8856 (mp10) cc_final: 0.8619 (mp10) REVERT: D 44 GLN cc_start: 0.9169 (tt0) cc_final: 0.8904 (tm-30) REVERT: D 83 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8308 (mmm-85) REVERT: D 90 GLU cc_start: 0.9261 (mp0) cc_final: 0.8584 (mp0) REVERT: D 110 GLU cc_start: 0.8946 (tp30) cc_final: 0.8673 (tp30) REVERT: D 117 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9117 (mtmt) REVERT: E 50 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 56 LYS cc_start: 0.9406 (mtpp) cc_final: 0.9125 (mtmm) REVERT: E 94 GLU cc_start: 0.8744 (tp30) cc_final: 0.8492 (tp30) REVERT: E 123 ASP cc_start: 0.9081 (m-30) cc_final: 0.8851 (m-30) REVERT: F 60 VAL cc_start: 0.9496 (p) cc_final: 0.8866 (m) REVERT: F 63 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8347 (mt-10) REVERT: F 64 ASN cc_start: 0.9189 (m-40) cc_final: 0.8905 (m110) REVERT: F 88 TYR cc_start: 0.8813 (m-10) cc_final: 0.7468 (m-10) REVERT: G 56 GLU cc_start: 0.9034 (tt0) cc_final: 0.8474 (tt0) REVERT: G 57 TYR cc_start: 0.9395 (t80) cc_final: 0.9067 (t80) REVERT: G 61 GLU cc_start: 0.9211 (tp30) cc_final: 0.8870 (tp30) REVERT: G 64 GLU cc_start: 0.8699 (tp30) cc_final: 0.8105 (tp30) REVERT: G 75 LYS cc_start: 0.9233 (mmtp) cc_final: 0.8858 (mmtp) REVERT: G 92 GLU cc_start: 0.7999 (pm20) cc_final: 0.7722 (pm20) REVERT: H 44 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8614 (tm-30) REVERT: H 80 TYR cc_start: 0.8660 (m-10) cc_final: 0.8188 (m-10) REVERT: H 83 ARG cc_start: 0.8822 (tpp80) cc_final: 0.8401 (tpp80) REVERT: H 85 THR cc_start: 0.8852 (m) cc_final: 0.8529 (p) REVERT: H 117 LYS cc_start: 0.9487 (mtmt) cc_final: 0.9258 (mtmt) outliers start: 16 outliers final: 12 residues processed: 251 average time/residue: 0.3041 time to fit residues: 101.2164 Evaluate side-chains 238 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU 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 F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 40 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.053067 restraints weight = 38347.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.054899 restraints weight = 19063.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056119 restraints weight = 12559.740| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10893 Z= 0.160 Angle : 0.629 10.446 15464 Z= 0.364 Chirality : 0.036 0.164 1715 Planarity : 0.003 0.029 1327 Dihedral : 28.664 89.903 3109 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.11 % Allowed : 27.68 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.29), residues: 829 helix: 2.27 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.38 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.011 0.001 PHE E 78 TYR 0.032 0.002 TYR D 80 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 624) hydrogen bonds : angle 3.06125 ( 1641) covalent geometry : bond 0.00356 (10892) covalent geometry : angle 0.62881 (15464) Misc. bond : bond 0.00089 ( 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 263 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.829 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: 0.9286 (tt0) cc_final: 0.8949 (tm-30) REVERT: B 20 LYS cc_start: 0.8595 (tppt) cc_final: 0.8084 (mmmm) REVERT: B 22 LEU cc_start: 0.8081 (tp) cc_final: 0.7845 (tp) REVERT: B 53 GLU cc_start: 0.9161 (tp30) cc_final: 0.8881 (tp30) REVERT: C 36 LYS cc_start: 0.9388 (mmmt) cc_final: 0.8983 (mmmm) REVERT: C 64 GLU cc_start: 0.8648 (tt0) cc_final: 0.7792 (tm-30) REVERT: C 73 ASN cc_start: 0.9041 (t0) cc_final: 0.8708 (t0) REVERT: C 84 GLN cc_start: 0.8516 (tp40) cc_final: 0.8060 (tp40) REVERT: C 89 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8774 (m-40) REVERT: C 104 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7610 (mm-40) REVERT: D 39 TYR cc_start: 0.8928 (t80) cc_final: 0.8540 (t80) REVERT: D 43 LYS cc_start: 0.9249 (ttmm) cc_final: 0.8874 (ttmm) REVERT: D 44 GLN cc_start: 0.9190 (tt0) cc_final: 0.8856 (tm-30) REVERT: D 90 GLU cc_start: 0.9268 (mp0) cc_final: 0.8551 (mp0) REVERT: D 102 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8468 (mm-30) REVERT: D 105 LYS cc_start: 0.9252 (ptpp) cc_final: 0.8904 (ptpp) REVERT: D 110 GLU cc_start: 0.8929 (tp30) cc_final: 0.8646 (tp30) REVERT: D 117 LYS cc_start: 0.9466 (mmmt) cc_final: 0.9125 (mtmt) REVERT: E 50 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8573 (mm-30) REVERT: E 86 SER cc_start: 0.9161 (m) cc_final: 0.8927 (p) REVERT: E 94 GLU cc_start: 0.8741 (tp30) cc_final: 0.8504 (tp30) REVERT: E 123 ASP cc_start: 0.9033 (m-30) cc_final: 0.8791 (m-30) REVERT: F 59 LYS cc_start: 0.9255 (tttm) cc_final: 0.8740 (tttm) REVERT: F 63 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8377 (mt-10) REVERT: F 64 ASN cc_start: 0.9145 (m-40) cc_final: 0.8899 (m110) REVERT: F 88 TYR cc_start: 0.8819 (m-10) cc_final: 0.7428 (m-10) REVERT: G 56 GLU cc_start: 0.9024 (tt0) cc_final: 0.8466 (tt0) REVERT: G 61 GLU cc_start: 0.9184 (tp30) cc_final: 0.8824 (tp30) REVERT: G 64 GLU cc_start: 0.8804 (tp30) cc_final: 0.8215 (tp30) REVERT: G 75 LYS cc_start: 0.9247 (mmtp) cc_final: 0.9037 (mmtp) REVERT: H 44 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8642 (tm-30) REVERT: H 54 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8689 (mtmt) REVERT: H 73 GLU cc_start: 0.8328 (tp30) cc_final: 0.8043 (tp30) REVERT: H 80 TYR cc_start: 0.8718 (m-10) cc_final: 0.8190 (m-10) REVERT: H 83 ARG cc_start: 0.8769 (tpp80) cc_final: 0.8451 (tpp80) REVERT: H 85 THR cc_start: 0.8856 (m) cc_final: 0.8557 (p) REVERT: H 117 LYS cc_start: 0.9492 (mtmt) cc_final: 0.9274 (mtmt) outliers start: 20 outliers final: 17 residues processed: 253 average time/residue: 0.2701 time to fit residues: 90.0728 Evaluate side-chains 248 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU 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 38 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain F residue 74 GLU 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 H residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.071848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050957 restraints weight = 38629.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.052715 restraints weight = 19503.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053859 restraints weight = 13010.695| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10893 Z= 0.232 Angle : 0.685 11.330 15464 Z= 0.392 Chirality : 0.038 0.160 1715 Planarity : 0.004 0.040 1327 Dihedral : 28.792 89.321 3109 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.04 % Allowed : 26.75 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.29), residues: 829 helix: 2.27 (0.21), residues: 559 sheet: None (None), residues: 0 loop : 0.01 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 79 PHE 0.010 0.002 PHE E 78 TYR 0.058 0.003 TYR B 88 ARG 0.012 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 624) hydrogen bonds : angle 3.33713 ( 1641) covalent geometry : bond 0.00519 (10892) covalent geometry : angle 0.68460 (15464) Misc. bond : bond 0.00105 ( 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 256 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.021 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: 0.9285 (tt0) cc_final: 0.8892 (tm-30) REVERT: B 20 LYS cc_start: 0.8754 (tppt) cc_final: 0.8182 (mmmm) REVERT: B 53 GLU cc_start: 0.9242 (tp30) cc_final: 0.8975 (tp30) REVERT: B 92 ARG cc_start: 0.8507 (tmm-80) cc_final: 0.8265 (tmm-80) REVERT: C 64 GLU cc_start: 0.8679 (tt0) cc_final: 0.7938 (tm-30) REVERT: C 73 ASN cc_start: 0.9046 (t0) cc_final: 0.8730 (t0) REVERT: C 84 GLN cc_start: 0.8601 (tp40) cc_final: 0.8136 (tp-100) REVERT: C 92 GLU cc_start: 0.8084 (pm20) cc_final: 0.7724 (pm20) REVERT: D 44 GLN cc_start: 0.9226 (tt0) cc_final: 0.8920 (tm-30) REVERT: D 90 GLU cc_start: 0.9281 (mp0) cc_final: 0.8551 (mp0) REVERT: D 110 GLU cc_start: 0.8989 (tp30) cc_final: 0.8734 (tp30) REVERT: D 117 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9155 (mtmt) REVERT: E 50 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8696 (mm-30) REVERT: E 56 LYS cc_start: 0.9450 (mtpp) cc_final: 0.9078 (mtmm) REVERT: E 123 ASP cc_start: 0.9097 (m-30) cc_final: 0.8827 (m-30) REVERT: F 63 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8349 (mt-10) REVERT: F 64 ASN cc_start: 0.9239 (m-40) cc_final: 0.8970 (m110) REVERT: F 88 TYR cc_start: 0.8886 (m-10) cc_final: 0.7974 (m-10) REVERT: G 56 GLU cc_start: 0.9037 (tt0) cc_final: 0.8484 (tt0) REVERT: G 61 GLU cc_start: 0.9193 (tp30) cc_final: 0.8848 (tp30) REVERT: G 64 GLU cc_start: 0.8833 (tp30) cc_final: 0.8180 (tp30) REVERT: G 75 LYS cc_start: 0.9286 (mmtp) cc_final: 0.9071 (mmtp) REVERT: G 92 GLU cc_start: 0.8122 (pm20) cc_final: 0.7820 (pm20) REVERT: H 44 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8651 (tm-30) REVERT: H 54 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8640 (mtmt) REVERT: H 83 ARG cc_start: 0.8838 (tpp80) cc_final: 0.8524 (tpp80) REVERT: H 85 THR cc_start: 0.8846 (m) cc_final: 0.8599 (p) REVERT: H 117 LYS cc_start: 0.9492 (mtmt) cc_final: 0.9244 (mtmt) outliers start: 26 outliers final: 23 residues processed: 244 average time/residue: 0.3008 time to fit residues: 97.8748 Evaluate side-chains 248 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 225 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 85 LEU 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 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 17 optimal weight: 0.0370 chunk 10 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.074498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053750 restraints weight = 37751.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.055563 restraints weight = 18733.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056790 restraints weight = 12319.424| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10893 Z= 0.160 Angle : 0.677 11.334 15464 Z= 0.385 Chirality : 0.037 0.165 1715 Planarity : 0.004 0.057 1327 Dihedral : 28.689 89.736 3109 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.42 % Allowed : 29.24 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.29), residues: 829 helix: 2.19 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.19 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS D 79 PHE 0.012 0.001 PHE E 78 TYR 0.061 0.002 TYR B 88 ARG 0.013 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 624) hydrogen bonds : angle 3.20578 ( 1641) covalent geometry : bond 0.00358 (10892) covalent geometry : angle 0.67715 (15464) Misc. bond : bond 0.00093 ( 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 266 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.836 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: 0.9256 (tt0) cc_final: 0.8888 (tm-30) REVERT: B 20 LYS cc_start: 0.8753 (tppt) cc_final: 0.8182 (mmmm) REVERT: B 53 GLU cc_start: 0.9175 (tp30) cc_final: 0.8899 (tp30) REVERT: B 92 ARG cc_start: 0.8424 (tmm-80) cc_final: 0.8139 (tmm-80) REVERT: C 35 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.7994 (tpt170) REVERT: C 36 LYS cc_start: 0.9322 (mmmm) cc_final: 0.8929 (tptt) REVERT: C 64 GLU cc_start: 0.8641 (tt0) cc_final: 0.7944 (tm-30) REVERT: C 73 ASN cc_start: 0.8984 (t0) cc_final: 0.8717 (t0) REVERT: C 84 GLN cc_start: 0.8454 (tp40) cc_final: 0.7989 (tp40) REVERT: C 104 GLN cc_start: 0.8346 (mm-40) cc_final: 0.7711 (mm-40) REVERT: D 39 TYR cc_start: 0.8914 (t80) cc_final: 0.8674 (t80) REVERT: D 44 GLN cc_start: 0.9237 (tt0) cc_final: 0.8878 (tm-30) REVERT: D 90 GLU cc_start: 0.9267 (mp0) cc_final: 0.8513 (mp0) REVERT: D 110 GLU cc_start: 0.8923 (tp30) cc_final: 0.8657 (tp30) REVERT: D 117 LYS cc_start: 0.9482 (mmmt) cc_final: 0.9090 (ttmt) REVERT: E 50 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8663 (mm-30) REVERT: E 56 LYS cc_start: 0.9438 (mtpp) cc_final: 0.9063 (mtmm) REVERT: E 123 ASP cc_start: 0.9047 (m-30) cc_final: 0.8814 (m-30) REVERT: F 63 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8287 (mt-10) REVERT: F 64 ASN cc_start: 0.9119 (m-40) cc_final: 0.8839 (m110) REVERT: G 56 GLU cc_start: 0.8998 (tt0) cc_final: 0.8451 (tt0) REVERT: G 61 GLU cc_start: 0.9186 (tp30) cc_final: 0.8830 (tp30) REVERT: G 64 GLU cc_start: 0.8773 (tp30) cc_final: 0.8202 (tp30) REVERT: G 75 LYS cc_start: 0.9262 (mmtp) cc_final: 0.9022 (mmtp) REVERT: H 44 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8599 (tm-30) REVERT: H 54 LYS cc_start: 0.8894 (mtmt) cc_final: 0.8632 (mtmt) REVERT: H 73 GLU cc_start: 0.8412 (tp30) cc_final: 0.8177 (tp30) REVERT: H 83 ARG cc_start: 0.8729 (tpp80) cc_final: 0.8401 (tpp80) REVERT: H 85 THR cc_start: 0.8738 (m) cc_final: 0.8498 (p) REVERT: H 117 LYS cc_start: 0.9486 (mtmt) cc_final: 0.9258 (mtmt) outliers start: 22 outliers final: 17 residues processed: 259 average time/residue: 0.2600 time to fit residues: 90.0901 Evaluate side-chains 252 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 235 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU 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 74 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS D 81 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.071977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050835 restraints weight = 38735.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052585 restraints weight = 19640.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.053721 restraints weight = 13119.627| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10893 Z= 0.246 Angle : 0.734 12.657 15464 Z= 0.413 Chirality : 0.040 0.162 1715 Planarity : 0.005 0.062 1327 Dihedral : 28.779 89.972 3109 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.27 % Allowed : 29.08 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.29), residues: 829 helix: 2.06 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -0.02 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 79 PHE 0.010 0.001 PHE E 78 TYR 0.078 0.003 TYR B 88 ARG 0.014 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 624) hydrogen bonds : angle 3.48165 ( 1641) covalent geometry : bond 0.00558 (10892) covalent geometry : angle 0.73358 (15464) Misc. bond : bond 0.00107 ( 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 249 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9289 (tt0) cc_final: 0.8890 (tm-30) REVERT: A 93 GLN cc_start: 0.9070 (tt0) cc_final: 0.8689 (tp40) REVERT: A 97 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7904 (mt-10) REVERT: B 20 LYS cc_start: 0.8780 (tppt) cc_final: 0.8254 (mmmm) REVERT: B 53 GLU cc_start: 0.9214 (tp30) cc_final: 0.8924 (tp30) REVERT: B 92 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.8085 (tmm-80) REVERT: C 32 ARG cc_start: 0.9038 (ttp-110) cc_final: 0.8598 (ttp80) REVERT: C 35 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7953 (tpt170) REVERT: C 36 LYS cc_start: 0.9328 (mmmm) cc_final: 0.8951 (tptt) REVERT: C 64 GLU cc_start: 0.8649 (tt0) cc_final: 0.7836 (tm-30) REVERT: C 73 ASN cc_start: 0.8990 (t0) cc_final: 0.8681 (t0) REVERT: C 84 GLN cc_start: 0.8627 (tp40) cc_final: 0.8120 (tp-100) REVERT: D 44 GLN cc_start: 0.9156 (tt0) cc_final: 0.8811 (tm-30) REVERT: D 90 GLU cc_start: 0.9322 (mp0) cc_final: 0.8545 (mp0) REVERT: D 110 GLU cc_start: 0.8956 (tp30) cc_final: 0.8704 (tp30) REVERT: D 117 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9116 (ttmt) REVERT: E 50 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8766 (mm-30) REVERT: E 123 ASP cc_start: 0.9116 (m-30) cc_final: 0.8820 (m-30) REVERT: F 63 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8559 (tm-30) REVERT: F 64 ASN cc_start: 0.9228 (m-40) cc_final: 0.8816 (m110) REVERT: F 88 TYR cc_start: 0.8520 (m-10) cc_final: 0.8197 (m-10) REVERT: G 56 GLU cc_start: 0.9001 (tt0) cc_final: 0.8449 (tt0) REVERT: G 61 GLU cc_start: 0.9191 (tp30) cc_final: 0.8843 (tp30) REVERT: G 64 GLU cc_start: 0.8824 (tp30) cc_final: 0.8242 (tp30) REVERT: G 75 LYS cc_start: 0.9277 (mmtp) cc_final: 0.9033 (mmtp) REVERT: H 37 TYR cc_start: 0.9170 (m-80) cc_final: 0.8952 (m-80) REVERT: H 44 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8627 (tm-30) REVERT: H 83 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8578 (tpp80) REVERT: H 85 THR cc_start: 0.8822 (m) cc_final: 0.8576 (p) REVERT: H 117 LYS cc_start: 0.9498 (mtmt) cc_final: 0.9232 (mtmt) outliers start: 21 outliers final: 19 residues processed: 240 average time/residue: 0.2550 time to fit residues: 81.6713 Evaluate side-chains 244 residues out of total 714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 85 LEU 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 74 ILE Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 74 GLU 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 H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 92 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN 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 = 0.3569 r_free = 0.3569 target = 0.073624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.052620 restraints weight = 38458.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054408 restraints weight = 19290.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055598 restraints weight = 12783.849| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10893 Z= 0.184 Angle : 0.724 12.341 15464 Z= 0.405 Chirality : 0.039 0.205 1715 Planarity : 0.004 0.062 1327 Dihedral : 28.734 89.436 3109 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.95 % Allowed : 30.17 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.29), residues: 829 helix: 2.10 (0.21), residues: 567 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 79 PHE 0.010 0.001 PHE E 78 TYR 0.060 0.003 TYR B 88 ARG 0.014 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 624) hydrogen bonds : angle 3.40742 ( 1641) covalent geometry : bond 0.00418 (10892) covalent geometry : angle 0.72401 (15464) Misc. bond : bond 0.00101 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.44 seconds wall clock time: 70 minutes 42.80 seconds (4242.80 seconds total)