Starting phenix.real_space_refine on Sun Mar 10 14:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/03_2024/8b3a_15824_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/03_2024/8b3a_15824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/03_2024/8b3a_15824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/03_2024/8b3a_15824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/03_2024/8b3a_15824_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/03_2024/8b3a_15824_updated.pdb" } resolution = 3.8 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= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 1320 2.51 5 N 450 2.21 5 O 240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2010 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "P" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "S" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "a" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "c" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Time building chain proxies: 1.20, per 1000 atoms: 0.60 Number of scatterers: 2010 At special positions: 0 Unit cell: (90.48, 49.92, 37.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 240 8.00 N 450 7.00 C 1320 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 229.8 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 240 1.27 - 1.34: 450 1.34 - 1.41: 180 1.41 - 1.47: 240 1.47 - 1.54: 930 Bond restraints: 2040 Sorted by residual: bond pdb=" C HIS I 4 " pdb=" N LEU I 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.16e+01 bond pdb=" C HIS U 4 " pdb=" N LEU U 5 " ideal model delta sigma weight residual 1.331 1.278 0.053 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS a 4 " pdb=" N LEU a 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS L 4 " pdb=" N LEU L 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.15e+01 bond pdb=" C HIS J 4 " pdb=" N LEU J 5 " ideal model delta sigma weight residual 1.331 1.279 0.052 1.55e-02 4.16e+03 1.14e+01 ... (remaining 2035 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.27: 160 106.27 - 112.56: 1088 112.56 - 118.85: 567 118.85 - 125.14: 825 125.14 - 131.43: 90 Bond angle restraints: 2730 Sorted by residual: angle pdb=" N LEU N 3 " pdb=" CA LEU N 3 " pdb=" C LEU N 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU M 3 " pdb=" CA LEU M 3 " pdb=" C LEU M 3 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU Y 3 " pdb=" CA LEU Y 3 " pdb=" C LEU Y 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU G 3 " pdb=" CA LEU G 3 " pdb=" C LEU G 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 angle pdb=" N LEU S 3 " pdb=" CA LEU S 3 " pdb=" C LEU S 3 " ideal model delta sigma weight residual 108.96 102.20 6.76 1.59e+00 3.96e-01 1.81e+01 ... (remaining 2725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.64: 860 18.64 - 37.29: 220 37.29 - 55.93: 60 55.93 - 74.57: 0 74.57 - 93.22: 30 Dihedral angle restraints: 1170 sinusoidal: 570 harmonic: 600 Sorted by residual: dihedral pdb=" CH3 ACE W 0 " pdb=" C ACE W 0 " pdb=" N LEU W 1 " pdb=" CA LEU W 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.78 -93.22 1 5.00e+00 4.00e-02 4.06e+02 dihedral pdb=" CH3 ACE K 0 " pdb=" C ACE K 0 " pdb=" N LEU K 1 " pdb=" CA LEU K 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.80 -93.20 1 5.00e+00 4.00e-02 4.05e+02 dihedral pdb=" CH3 ACE c 0 " pdb=" C ACE c 0 " pdb=" N LEU c 1 " pdb=" CA LEU c 1 " ideal model delta sinusoidal sigma weight residual -180.00 -86.82 -93.18 1 5.00e+00 4.00e-02 4.05e+02 ... (remaining 1167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 170 0.041 - 0.082: 40 0.082 - 0.123: 30 0.123 - 0.164: 17 0.164 - 0.205: 73 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA HIS V 4 " pdb=" N HIS V 4 " pdb=" C HIS V 4 " pdb=" CB HIS V 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS F 4 " pdb=" N HIS F 4 " pdb=" C HIS F 4 " pdb=" CB HIS F 4 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA HIS U 4 " pdb=" N HIS U 4 " pdb=" C HIS U 4 " pdb=" CB HIS U 4 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 327 not shown) Planarity restraints: 330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE J 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE J 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE J 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU J 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU J 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE V 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE V 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE V 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU V 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU V 1 " -0.366 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE P 0 " 0.089 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" O ACE P 0 " -0.104 2.00e-02 2.50e+03 pdb=" CH3 ACE P 0 " -0.175 2.00e-02 2.50e+03 pdb=" N LEU P 1 " 0.556 2.00e-02 2.50e+03 pdb=" CA LEU P 1 " -0.366 2.00e-02 2.50e+03 ... (remaining 327 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 758 3.07 - 3.53: 2022 3.53 - 3.99: 2661 3.99 - 4.44: 3385 4.44 - 4.90: 6093 Nonbonded interactions: 14919 Sorted by model distance: nonbonded pdb=" N LEU Y 5 " pdb=" O LEU Y 5 " model vdw 2.613 2.496 nonbonded pdb=" N LEU A 5 " pdb=" O LEU A 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU B 5 " pdb=" O LEU B 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU Z 5 " pdb=" O LEU Z 5 " model vdw 2.614 2.496 nonbonded pdb=" N LEU M 5 " pdb=" O LEU M 5 " model vdw 2.614 2.496 ... (remaining 14914 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 0.010 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.640 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 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 0.053 2040 Z= 0.635 Angle : 1.879 7.587 2730 Z= 1.064 Chirality : 0.104 0.205 330 Planarity : 0.094 0.314 330 Dihedral : 27.060 93.216 750 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 42.86 % Favored : 57.14 % 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: -4.71 (0.30), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.23), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 2 ARG 0.002 0.000 ARG c 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2 time to evaluate : 0.231 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.8365 time to fit residues: 2.0920 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 1.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.272 2040 Z= 3.993 Angle : 5.815 32.386 2730 Z= 2.692 Chirality : 0.411 1.286 330 Planarity : 0.051 0.174 330 Dihedral : 10.239 30.873 270 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 290.15 Ramachandran Plot: Outliers : 61.33 % Allowed : 29.33 % Favored : 9.33 % Rotamer: Outliers : 50.95 % Allowed : 23.33 % Favored : 25.71 % Cbeta Deviations : 9.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -10.69 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.15 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.050 0.014 HIS U 4 ARG 0.011 0.002 ARG c 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 0 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7764 (t-170) REVERT: A 7 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8150 (tt) REVERT: B 2 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7788 (t-170) REVERT: B 7 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8136 (tt) REVERT: D 1 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8075 (pp) REVERT: G 5 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8432 (tt) REVERT: G 7 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8494 (tt) REVERT: H 5 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8344 (tt) REVERT: I 6 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8250 (ttt180) REVERT: I 7 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (tt) REVERT: J 7 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8119 (tt) REVERT: K 7 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7175 (tt) REVERT: L 7 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7137 (tt) REVERT: M 2 HIS cc_start: 0.9201 (OUTLIER) cc_final: 0.8810 (t-170) REVERT: M 5 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8529 (tt) REVERT: N 2 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8810 (t-170) REVERT: O 4 HIS cc_start: 0.9290 (OUTLIER) cc_final: 0.8911 (m90) REVERT: O 7 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8410 (tt) REVERT: P 2 HIS cc_start: 0.8914 (OUTLIER) cc_final: 0.8032 (t-170) REVERT: P 4 HIS cc_start: 0.9271 (OUTLIER) cc_final: 0.8261 (t70) REVERT: P 6 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8268 (tmt-80) REVERT: P 7 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8361 (tt) REVERT: Q 7 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7375 (tt) REVERT: V 6 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8128 (tmt-80) REVERT: X 4 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8722 (t70) REVERT: a 7 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7662 (tt) REVERT: b 6 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7390 (tmt-80) REVERT: b 7 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7619 (tt) outliers start: 107 outliers final: 32 residues processed: 107 average time/residue: 0.1288 time to fit residues: 16.0183 Evaluate side-chains 65 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 5 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain d residue 2 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 1.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.281 2040 Z= 3.935 Angle : 6.039 33.845 2730 Z= 2.735 Chirality : 0.413 1.308 330 Planarity : 0.050 0.159 330 Dihedral : 10.665 33.050 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 296.75 Ramachandran Plot: Outliers : 51.33 % Allowed : 44.00 % Favored : 4.67 % Rotamer: Outliers : 62.38 % Allowed : 19.52 % Favored : 18.10 % Cbeta Deviations : 13.81 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % 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: -10.75 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.19 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.013 HIS D 4 ARG 0.010 0.002 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 0 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7625 (t-170) REVERT: A 5 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7868 (tt) REVERT: B 2 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.7549 (t-170) REVERT: B 5 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7919 (tt) REVERT: D 5 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8378 (tt) REVERT: E 2 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7741 (t-170) REVERT: F 2 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7827 (t-170) REVERT: G 5 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8173 (tt) REVERT: G 6 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8166 (ttm170) REVERT: H 4 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8174 (t70) REVERT: H 5 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8259 (tt) REVERT: I 7 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8283 (tt) REVERT: J 7 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8190 (tt) REVERT: K 4 HIS cc_start: 0.9081 (OUTLIER) cc_final: 0.8439 (t70) REVERT: K 5 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8825 (tt) REVERT: K 7 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6870 (tt) REVERT: L 5 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8747 (tt) REVERT: L 7 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7116 (tt) REVERT: M 2 HIS cc_start: 0.9232 (OUTLIER) cc_final: 0.8794 (t-170) REVERT: M 5 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8602 (tt) REVERT: M 6 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8703 (ttm170) REVERT: N 5 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8552 (tt) REVERT: O 2 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8452 (t-170) REVERT: O 4 HIS cc_start: 0.9461 (OUTLIER) cc_final: 0.8538 (t70) REVERT: P 2 HIS cc_start: 0.8986 (OUTLIER) cc_final: 0.8232 (t-170) REVERT: P 4 HIS cc_start: 0.9332 (OUTLIER) cc_final: 0.8339 (t70) REVERT: P 7 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8539 (tt) REVERT: Q 5 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9096 (tt) REVERT: S 6 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8012 (ttt-90) REVERT: T 6 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: Y 2 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8189 (t-170) REVERT: Y 7 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7970 (tt) REVERT: Z 7 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8035 (tt) REVERT: a 4 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.7559 (t70) REVERT: a 7 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7560 (tt) REVERT: b 4 HIS cc_start: 0.8485 (OUTLIER) cc_final: 0.7276 (t70) REVERT: b 7 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7878 (tt) REVERT: c 5 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8324 (tt) REVERT: d 5 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8269 (tt) outliers start: 131 outliers final: 59 residues processed: 131 average time/residue: 0.1621 time to fit residues: 23.6975 Evaluate side-chains 104 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 6 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 2 HIS Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 1 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 5 LEU Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 1.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.284 2040 Z= 3.911 Angle : 5.925 33.428 2730 Z= 2.715 Chirality : 0.414 1.302 330 Planarity : 0.049 0.157 330 Dihedral : 10.240 34.259 270 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 301.66 Ramachandran Plot: Outliers : 44.00 % Allowed : 52.00 % Favored : 4.00 % Rotamer: Outliers : 66.67 % Allowed : 14.76 % Favored : 18.57 % Cbeta Deviations : 10.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % 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: -10.75 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.19 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.050 0.013 HIS D 4 ARG 0.018 0.003 ARG H 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 0 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7549 (t-170) REVERT: A 5 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 2 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7532 (t-170) REVERT: B 5 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7932 (tt) REVERT: C 2 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.6807 (t-170) REVERT: D 2 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.6779 (t-170) REVERT: E 2 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7831 (t-170) REVERT: F 2 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7920 (t-170) REVERT: G 5 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8264 (tt) REVERT: G 6 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8285 (ttm170) REVERT: G 7 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8385 (tt) REVERT: H 5 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8227 (tt) REVERT: I 4 HIS cc_start: 0.8927 (OUTLIER) cc_final: 0.8348 (t70) REVERT: I 7 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8161 (tt) REVERT: J 7 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8257 (tt) REVERT: K 4 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8486 (t70) REVERT: K 7 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.7040 (tt) REVERT: L 5 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8795 (tt) REVERT: M 2 HIS cc_start: 0.9189 (OUTLIER) cc_final: 0.8263 (t-170) REVERT: M 4 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.7939 (t70) REVERT: M 5 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8604 (tt) REVERT: M 7 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8604 (tt) REVERT: N 4 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.7946 (t70) REVERT: N 5 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (tt) REVERT: N 7 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8581 (tt) REVERT: O 2 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8702 (t-170) REVERT: P 2 HIS cc_start: 0.8918 (OUTLIER) cc_final: 0.8062 (t-170) REVERT: P 4 HIS cc_start: 0.9312 (OUTLIER) cc_final: 0.8279 (t70) REVERT: P 7 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8380 (tt) REVERT: Q 5 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9098 (tt) REVERT: R 5 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8959 (tt) REVERT: Y 7 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8067 (tt) REVERT: Z 7 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8068 (tt) REVERT: a 4 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.7909 (t70) REVERT: a 7 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7685 (tt) REVERT: b 4 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.7433 (t70) REVERT: b 6 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7812 (ttt-90) REVERT: b 7 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7670 (tt) outliers start: 140 outliers final: 65 residues processed: 140 average time/residue: 0.2072 time to fit residues: 32.3528 Evaluate side-chains 106 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 3 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 1.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.283 2040 Z= 3.884 Angle : 5.920 33.496 2730 Z= 2.726 Chirality : 0.419 1.306 330 Planarity : 0.049 0.170 330 Dihedral : 10.238 34.435 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 299.76 Ramachandran Plot: Outliers : 44.00 % Allowed : 51.33 % Favored : 4.67 % Rotamer: Outliers : 66.19 % Allowed : 13.33 % Favored : 20.48 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.19 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.051 0.013 HIS D 4 ARG 0.011 0.002 ARG P 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 0 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7562 (t-170) REVERT: A 5 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 2 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7520 (t-170) REVERT: B 5 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7911 (tt) REVERT: C 2 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.6801 (t-170) REVERT: D 2 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.6700 (t-170) REVERT: E 2 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7934 (t-170) REVERT: E 7 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6296 (tt) REVERT: F 2 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7878 (t-170) REVERT: G 5 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8244 (tt) REVERT: G 6 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8306 (ttm170) REVERT: H 5 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (tt) REVERT: I 4 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8299 (t70) REVERT: I 7 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8241 (tt) REVERT: J 7 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8267 (tt) REVERT: K 4 HIS cc_start: 0.9032 (OUTLIER) cc_final: 0.8368 (t70) REVERT: K 7 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6821 (tt) REVERT: M 2 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8281 (t-170) REVERT: M 4 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.7952 (t70) REVERT: M 5 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8618 (tt) REVERT: M 7 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8607 (tt) REVERT: N 4 HIS cc_start: 0.9099 (OUTLIER) cc_final: 0.7984 (t70) REVERT: N 5 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8617 (tt) REVERT: N 7 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8594 (tt) REVERT: O 2 HIS cc_start: 0.9087 (OUTLIER) cc_final: 0.8686 (t-170) REVERT: P 2 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8050 (t-170) REVERT: P 4 HIS cc_start: 0.9361 (OUTLIER) cc_final: 0.8319 (t70) REVERT: P 7 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8337 (tt) REVERT: R 5 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8969 (tt) REVERT: X 7 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7269 (tt) REVERT: Y 7 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8071 (tt) REVERT: Z 7 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8043 (tt) REVERT: a 4 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.7992 (t70) REVERT: a 7 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7655 (tt) REVERT: b 4 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7617 (t70) REVERT: b 7 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7659 (tt) outliers start: 139 outliers final: 73 residues processed: 139 average time/residue: 0.1794 time to fit residues: 27.4454 Evaluate side-chains 113 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 4 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain X residue 7 LEU Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 1.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.291 2040 Z= 3.880 Angle : 5.970 33.395 2730 Z= 2.737 Chirality : 0.422 1.304 330 Planarity : 0.048 0.157 330 Dihedral : 10.387 34.795 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 296.68 Ramachandran Plot: Outliers : 44.00 % Allowed : 52.00 % Favored : 4.00 % Rotamer: Outliers : 64.29 % Allowed : 16.19 % Favored : 19.52 % Cbeta Deviations : 10.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.11 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.051 0.013 HIS D 4 ARG 0.011 0.002 ARG b 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 0 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7669 (t-170) REVERT: A 5 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 2 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7655 (t-170) REVERT: B 5 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7885 (tt) REVERT: C 2 HIS cc_start: 0.7920 (OUTLIER) cc_final: 0.6740 (t-170) REVERT: D 2 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.6657 (t-170) REVERT: E 2 HIS cc_start: 0.8352 (OUTLIER) cc_final: 0.7966 (t-170) REVERT: F 2 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7929 (t-170) REVERT: G 5 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8250 (tt) REVERT: G 6 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8317 (ttm170) REVERT: H 5 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8188 (tt) REVERT: I 4 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.8235 (t70) REVERT: I 7 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8256 (tt) REVERT: J 4 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8479 (t70) REVERT: J 7 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8247 (tt) REVERT: K 4 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8345 (t70) REVERT: K 5 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (tt) REVERT: K 7 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6921 (tt) REVERT: L 5 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8841 (tt) REVERT: M 2 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8289 (t-170) REVERT: M 4 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.7949 (t70) REVERT: M 5 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8622 (tt) REVERT: M 7 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8622 (tt) REVERT: N 4 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.8023 (t70) REVERT: N 5 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (tt) REVERT: N 7 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (tt) REVERT: O 2 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8707 (t-170) REVERT: P 2 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8088 (t-170) REVERT: P 4 HIS cc_start: 0.9357 (OUTLIER) cc_final: 0.8342 (t70) REVERT: P 7 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8269 (tt) REVERT: R 5 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8937 (tt) REVERT: Y 7 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8093 (tt) REVERT: Z 7 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8056 (tt) REVERT: a 4 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.7973 (t70) REVERT: a 7 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7707 (tt) REVERT: b 4 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7726 (t70) REVERT: b 7 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7726 (tt) outliers start: 135 outliers final: 77 residues processed: 135 average time/residue: 0.1866 time to fit residues: 27.6039 Evaluate side-chains 119 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 5 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 1.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.285 2040 Z= 3.876 Angle : 5.989 33.434 2730 Z= 2.746 Chirality : 0.422 1.311 330 Planarity : 0.047 0.157 330 Dihedral : 10.370 35.048 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 298.34 Ramachandran Plot: Outliers : 44.00 % Allowed : 52.00 % Favored : 4.00 % Rotamer: Outliers : 60.48 % Allowed : 18.10 % Favored : 21.43 % Cbeta Deviations : 10.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.051 0.013 HIS D 4 ARG 0.012 0.002 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 0 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.7662 (t-170) REVERT: A 5 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7912 (tt) REVERT: B 2 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7655 (t-170) REVERT: B 5 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7905 (tt) REVERT: C 2 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.6672 (t-170) REVERT: D 2 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.6702 (t-170) REVERT: E 2 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7931 (t-170) REVERT: F 2 HIS cc_start: 0.8286 (OUTLIER) cc_final: 0.7928 (t-170) REVERT: G 5 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8273 (tt) REVERT: G 6 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8276 (ttm170) REVERT: H 5 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8204 (tt) REVERT: I 4 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8259 (t70) REVERT: I 7 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8161 (tt) REVERT: J 4 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.8422 (t70) REVERT: J 7 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8221 (tt) REVERT: K 4 HIS cc_start: 0.9049 (OUTLIER) cc_final: 0.8368 (t70) REVERT: M 2 HIS cc_start: 0.9203 (OUTLIER) cc_final: 0.8305 (t-170) REVERT: M 4 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.7944 (t70) REVERT: M 5 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8639 (tt) REVERT: N 4 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.8027 (t70) REVERT: N 5 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8621 (tt) REVERT: O 2 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8660 (t-170) REVERT: P 2 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.8122 (t-170) REVERT: P 4 HIS cc_start: 0.9334 (OUTLIER) cc_final: 0.8331 (t70) REVERT: P 7 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8309 (tt) REVERT: Q 5 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8969 (tt) REVERT: R 5 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8953 (tt) REVERT: Y 7 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8063 (tt) REVERT: Z 7 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8036 (tt) REVERT: a 4 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8017 (t70) REVERT: a 7 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7596 (tt) REVERT: b 4 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7853 (t70) REVERT: b 7 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7718 (tt) outliers start: 127 outliers final: 77 residues processed: 127 average time/residue: 0.1952 time to fit residues: 27.3402 Evaluate side-chains 114 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 4 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 1.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.283 2040 Z= 3.868 Angle : 6.001 33.417 2730 Z= 2.752 Chirality : 0.421 1.308 330 Planarity : 0.047 0.157 330 Dihedral : 10.493 35.118 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 297.63 Ramachandran Plot: Outliers : 44.00 % Allowed : 52.00 % Favored : 4.00 % Rotamer: Outliers : 60.00 % Allowed : 15.24 % Favored : 24.76 % Cbeta Deviations : 10.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.67 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.051 0.013 HIS D 4 ARG 0.012 0.002 ARG F 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 0 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.7545 (t-170) REVERT: A 5 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7913 (tt) REVERT: B 2 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7543 (t-170) REVERT: B 5 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7918 (tt) REVERT: C 2 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.6652 (t-170) REVERT: D 2 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.6697 (t-170) REVERT: E 2 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.7990 (t-170) REVERT: E 7 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6232 (tt) REVERT: F 2 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7939 (t-170) REVERT: G 5 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8242 (tt) REVERT: G 6 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8267 (ttm170) REVERT: H 5 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8220 (tt) REVERT: I 4 HIS cc_start: 0.8961 (OUTLIER) cc_final: 0.8269 (t70) REVERT: I 7 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (tt) REVERT: J 4 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8425 (t70) REVERT: J 7 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8205 (tt) REVERT: K 4 HIS cc_start: 0.9022 (OUTLIER) cc_final: 0.8359 (t70) REVERT: L 7 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6899 (tt) REVERT: M 2 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8314 (t-170) REVERT: M 4 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.7941 (t70) REVERT: M 5 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8626 (tt) REVERT: N 4 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8015 (t70) REVERT: N 5 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8605 (tt) REVERT: O 2 HIS cc_start: 0.9096 (OUTLIER) cc_final: 0.8654 (t-170) REVERT: P 2 HIS cc_start: 0.8968 (OUTLIER) cc_final: 0.8522 (t-170) REVERT: P 7 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8378 (tt) REVERT: Q 5 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9017 (tt) REVERT: Y 7 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8081 (tt) REVERT: Z 7 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8076 (tt) REVERT: a 4 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.7992 (t70) REVERT: a 7 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7624 (tt) REVERT: b 4 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.7871 (t70) REVERT: b 7 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7710 (tt) outliers start: 126 outliers final: 78 residues processed: 126 average time/residue: 0.2083 time to fit residues: 28.7228 Evaluate side-chains 114 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 3 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 1.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.284 2040 Z= 3.862 Angle : 6.019 33.457 2730 Z= 2.758 Chirality : 0.424 1.307 330 Planarity : 0.047 0.156 330 Dihedral : 10.594 35.473 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 298.10 Ramachandran Plot: Outliers : 43.33 % Allowed : 52.67 % Favored : 4.00 % Rotamer: Outliers : 58.10 % Allowed : 17.14 % Favored : 24.76 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS D 4 ARG 0.012 0.002 ARG c 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 0 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7549 (t-170) REVERT: A 5 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7889 (tt) REVERT: B 2 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7533 (t-170) REVERT: B 5 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7897 (tt) REVERT: C 2 HIS cc_start: 0.7869 (OUTLIER) cc_final: 0.6637 (t-170) REVERT: D 2 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.6705 (t-170) REVERT: E 2 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.8024 (t-170) REVERT: E 7 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6177 (tt) REVERT: F 2 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7993 (t-170) REVERT: G 5 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8257 (tt) REVERT: G 6 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8261 (ttm170) REVERT: H 5 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8217 (tt) REVERT: I 4 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8210 (t70) REVERT: I 7 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8200 (tt) REVERT: J 4 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.8363 (t70) REVERT: J 7 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8183 (tt) REVERT: K 4 HIS cc_start: 0.9007 (OUTLIER) cc_final: 0.8290 (t70) REVERT: L 7 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6934 (tt) REVERT: M 2 HIS cc_start: 0.9217 (OUTLIER) cc_final: 0.8323 (t-170) REVERT: M 4 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.7939 (t70) REVERT: M 5 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8638 (tt) REVERT: N 2 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8224 (t-170) REVERT: N 4 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.7959 (t70) REVERT: N 5 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8628 (tt) REVERT: O 2 HIS cc_start: 0.9094 (OUTLIER) cc_final: 0.8670 (t-170) REVERT: P 2 HIS cc_start: 0.8967 (OUTLIER) cc_final: 0.8513 (t-170) REVERT: P 7 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8307 (tt) REVERT: Q 5 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9023 (tt) REVERT: Y 7 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (tt) REVERT: Z 7 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8060 (tt) REVERT: a 4 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.7993 (t70) REVERT: a 7 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7598 (tt) REVERT: b 4 HIS cc_start: 0.8642 (OUTLIER) cc_final: 0.7929 (t70) REVERT: b 7 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7668 (tt) outliers start: 122 outliers final: 78 residues processed: 122 average time/residue: 0.1957 time to fit residues: 26.1630 Evaluate side-chains 113 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 1.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.284 2040 Z= 3.864 Angle : 6.044 33.464 2730 Z= 2.766 Chirality : 0.425 1.310 330 Planarity : 0.047 0.158 330 Dihedral : 10.633 35.562 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 299.53 Ramachandran Plot: Outliers : 43.33 % Allowed : 52.67 % Favored : 4.00 % Rotamer: Outliers : 55.71 % Allowed : 20.48 % Favored : 23.81 % Cbeta Deviations : 10.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS D 4 ARG 0.016 0.002 ARG c 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 0 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7564 (t-170) REVERT: A 5 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 2 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7549 (t-170) REVERT: B 5 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7910 (tt) REVERT: C 2 HIS cc_start: 0.7864 (OUTLIER) cc_final: 0.6659 (t-170) REVERT: D 2 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.6650 (t-170) REVERT: E 2 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.8028 (t-170) REVERT: E 7 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6252 (tt) REVERT: F 2 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.8029 (t-170) REVERT: G 5 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8249 (tt) REVERT: G 6 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8259 (ttm170) REVERT: H 5 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8230 (tt) REVERT: I 4 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8218 (t70) REVERT: I 7 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8198 (tt) REVERT: J 4 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8355 (t70) REVERT: J 7 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8194 (tt) REVERT: K 4 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8285 (t70) REVERT: L 7 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6914 (tt) REVERT: M 2 HIS cc_start: 0.9221 (OUTLIER) cc_final: 0.8324 (t-170) REVERT: M 4 HIS cc_start: 0.9082 (OUTLIER) cc_final: 0.7938 (t70) REVERT: M 5 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8642 (tt) REVERT: N 2 HIS cc_start: 0.9187 (OUTLIER) cc_final: 0.8239 (t-170) REVERT: N 4 HIS cc_start: 0.9086 (OUTLIER) cc_final: 0.7950 (t70) REVERT: O 2 HIS cc_start: 0.9091 (OUTLIER) cc_final: 0.8646 (t-170) REVERT: P 2 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8521 (t-170) REVERT: P 7 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8392 (tt) REVERT: Q 5 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9013 (tt) REVERT: Y 7 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8020 (tt) REVERT: Z 7 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8064 (tt) REVERT: a 4 HIS cc_start: 0.8796 (OUTLIER) cc_final: 0.7909 (t70) REVERT: a 7 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7595 (tt) REVERT: b 4 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.7981 (t70) REVERT: b 7 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7697 (tt) outliers start: 117 outliers final: 77 residues processed: 117 average time/residue: 0.2161 time to fit residues: 27.5500 Evaluate side-chains 110 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 0 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain B residue 1 LEU Chi-restraints excluded: chain B residue 2 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain C residue 1 LEU Chi-restraints excluded: chain C residue 2 HIS Chi-restraints excluded: chain C residue 4 HIS Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 2 HIS Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 4 HIS Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain G residue 1 LEU Chi-restraints excluded: chain G residue 2 HIS Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain H residue 1 LEU Chi-restraints excluded: chain H residue 2 HIS Chi-restraints excluded: chain H residue 4 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain I residue 1 LEU Chi-restraints excluded: chain I residue 2 HIS Chi-restraints excluded: chain I residue 4 HIS Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 2 HIS Chi-restraints excluded: chain J residue 4 HIS Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain K residue 1 LEU Chi-restraints excluded: chain K residue 4 HIS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain L residue 1 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 4 HIS Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 4 HIS Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain O residue 1 LEU Chi-restraints excluded: chain O residue 2 HIS Chi-restraints excluded: chain O residue 4 HIS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain P residue 1 LEU Chi-restraints excluded: chain P residue 2 HIS Chi-restraints excluded: chain P residue 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 2 HIS Chi-restraints excluded: chain Q residue 4 HIS Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 1 LEU Chi-restraints excluded: chain T residue 2 HIS Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain U residue 1 LEU Chi-restraints excluded: chain U residue 4 HIS Chi-restraints excluded: chain V residue 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 6 ARG Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain a residue 1 LEU Chi-restraints excluded: chain a residue 4 HIS Chi-restraints excluded: chain a residue 6 ARG Chi-restraints excluded: chain a residue 7 LEU Chi-restraints excluded: chain b residue 1 LEU Chi-restraints excluded: chain b residue 4 HIS Chi-restraints excluded: chain b residue 6 ARG Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain c residue 6 ARG Chi-restraints excluded: chain d residue 1 LEU Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 6 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 2.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 4 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 = 0.4293 r_free = 0.4293 target = 0.084217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.069382 restraints weight = 6488.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.070894 restraints weight = 4325.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.072073 restraints weight = 3158.792| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5823 moved from start: 1.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.297 2040 Z= 3.864 Angle : 6.036 33.507 2730 Z= 2.768 Chirality : 0.425 1.308 330 Planarity : 0.047 0.158 330 Dihedral : 10.713 36.317 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 300.95 Ramachandran Plot: Outliers : 43.33 % Allowed : 52.67 % Favored : 4.00 % Rotamer: Outliers : 53.33 % Allowed : 21.90 % Favored : 24.76 % Cbeta Deviations : 11.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -10.74 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS D 4 ARG 0.016 0.002 ARG c 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 855.46 seconds wall clock time: 16 minutes 24.46 seconds (984.46 seconds total)