Starting phenix.real_space_refine on Wed Jan 17 10:56:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/01_2024/8b3a_15824_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/01_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_15824/01_2024/8b3a_15824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/01_2024/8b3a_15824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/01_2024/8b3a_15824_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/01_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-1.21-5211/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: 1.15, per 1000 atoms: 0.57 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: 0.82 Conformation dependent library (CDL) restraints added in 230.5 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: 0.27 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: 0.86 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 LEU T 7 " pdb=" N NH2 T 8 " ideal model delta sigma weight residual 2.329 1.328 1.001 1.40e-02 5.10e+03 5.12e+03 bond pdb=" C LEU G 7 " pdb=" N NH2 G 8 " ideal model delta sigma weight residual 2.329 1.328 1.001 1.40e-02 5.10e+03 5.11e+03 bond pdb=" C LEU S 7 " pdb=" N NH2 S 8 " ideal model delta sigma weight residual 2.329 1.328 1.001 1.40e-02 5.10e+03 5.11e+03 bond pdb=" C LEU Z 7 " pdb=" N NH2 Z 8 " ideal model delta sigma weight residual 2.329 1.328 1.001 1.40e-02 5.10e+03 5.11e+03 bond pdb=" C LEU M 7 " pdb=" N NH2 M 8 " ideal model delta sigma weight residual 2.329 1.328 1.001 1.40e-02 5.10e+03 5.11e+03 ... (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: 0.000 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: 0.000 Extract box with map and model: 1.670 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.480 Find NCS groups from input model: 0.190 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- 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 : 0.122 1.001 2040 Z= 8.685 Angle : 1.892 7.587 2730 Z= 1.067 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 : 0.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.8792 time to fit residues: 2.1869 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 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 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: 0.8228 moved from start: 1.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.255 2040 Z= 4.009 Angle : 5.833 31.517 2730 Z= 2.729 Chirality : 0.409 1.271 330 Planarity : 0.051 0.176 330 Dihedral : 10.568 31.603 270 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 291.37 Ramachandran Plot: Outliers : 59.33 % Allowed : 28.00 % Favored : 12.67 % Rotamer: Outliers : 49.05 % Allowed : 23.81 % Favored : 27.14 % Cbeta Deviations : 9.05 % 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: -10.67 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.13 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS O 4 ARG 0.014 0.002 ARG d 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 103 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 0 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7845 (t-170) REVERT: A 7 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 7 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7894 (tt) REVERT: E 5 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8105 (tt) REVERT: E 7 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6737 (tt) REVERT: G 5 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8371 (tt) REVERT: G 7 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8386 (tt) REVERT: H 7 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8490 (tt) REVERT: I 6 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8272 (ttt180) REVERT: I 7 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8202 (tt) REVERT: J 7 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8369 (tt) REVERT: K 5 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8739 (tt) REVERT: K 7 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7292 (tt) REVERT: M 2 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8809 (t-170) REVERT: M 7 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8613 (tt) REVERT: N 2 HIS cc_start: 0.9161 (OUTLIER) cc_final: 0.8781 (t-170) REVERT: N 7 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8610 (tt) REVERT: O 4 HIS cc_start: 0.9311 (OUTLIER) cc_final: 0.8906 (m90) REVERT: O 7 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8575 (tt) REVERT: P 4 HIS cc_start: 0.9304 (OUTLIER) cc_final: 0.8560 (t70) REVERT: P 6 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8379 (tmt-80) REVERT: P 7 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8389 (tt) REVERT: Q 5 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8977 (tt) REVERT: X 4 HIS cc_start: 0.9116 (OUTLIER) cc_final: 0.8614 (t70) REVERT: a 6 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7505 (ttt-90) REVERT: a 7 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7859 (tt) REVERT: b 6 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7601 (tmt-80) REVERT: b 7 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7847 (tt) REVERT: d 7 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6668 (tt) outliers start: 103 outliers final: 39 residues processed: 103 average time/residue: 0.1220 time to fit residues: 14.5570 Evaluate side-chains 69 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 7 LEU 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 2 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 7 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 7 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 5 LEU Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 4 HIS Chi-restraints excluded: chain M residue 1 LEU Chi-restraints excluded: chain M residue 2 HIS Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain N residue 1 LEU Chi-restraints excluded: chain N residue 2 HIS Chi-restraints excluded: chain N residue 7 LEU 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 4 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 5 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 U residue 4 HIS Chi-restraints excluded: chain V residue 2 HIS Chi-restraints excluded: chain X residue 4 HIS Chi-restraints excluded: chain Y residue 1 LEU Chi-restraints excluded: chain Y residue 2 HIS 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 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 d residue 2 HIS Chi-restraints excluded: chain d residue 7 LEU 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** ** 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: 0.8236 moved from start: 1.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.289 2040 Z= 3.917 Angle : 5.954 33.231 2730 Z= 2.718 Chirality : 0.409 1.309 330 Planarity : 0.051 0.171 330 Dihedral : 10.636 33.212 270 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 291.71 Ramachandran Plot: Outliers : 50.67 % Allowed : 45.33 % Favored : 4.00 % Rotamer: Outliers : 60.95 % Allowed : 18.57 % Favored : 20.48 % Cbeta Deviations : 11.90 % 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 0.051 0.014 HIS C 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 128 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 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: 0.8392 (OUTLIER) cc_final: 0.7826 (t-170) REVERT: A 5 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7860 (tt) REVERT: A 7 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 2 HIS cc_start: 0.8388 (OUTLIER) cc_final: 0.7536 (t-170) REVERT: B 5 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7818 (tt) REVERT: B 7 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7961 (tt) REVERT: C 2 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7250 (t-170) REVERT: C 4 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7302 (m90) REVERT: E 2 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7688 (t-170) REVERT: E 5 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8331 (tt) REVERT: F 2 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7861 (t-170) REVERT: G 5 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8113 (tt) REVERT: H 5 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8100 (tt) REVERT: I 7 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8283 (tt) REVERT: J 7 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8243 (tt) REVERT: K 5 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8662 (tt) REVERT: K 7 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7354 (tt) REVERT: L 5 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8766 (tt) REVERT: L 7 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7314 (tt) REVERT: M 2 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8818 (t-170) REVERT: M 5 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8570 (tt) REVERT: N 2 HIS cc_start: 0.9188 (OUTLIER) cc_final: 0.8810 (t-170) REVERT: N 5 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8558 (tt) REVERT: O 2 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8575 (t-170) REVERT: P 2 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8180 (t-170) REVERT: P 4 HIS cc_start: 0.9302 (OUTLIER) cc_final: 0.8354 (t70) REVERT: P 7 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8430 (tt) REVERT: Q 5 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9024 (tt) REVERT: R 5 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8955 (tt) REVERT: S 6 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8233 (ttt-90) REVERT: T 6 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8165 (ttt-90) REVERT: X 6 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8124 (tmt-80) REVERT: Y 2 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7942 (t70) REVERT: Y 7 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8236 (tt) REVERT: a 4 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7707 (t70) REVERT: a 7 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7658 (tt) REVERT: b 4 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.7351 (t70) REVERT: b 7 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7709 (tt) REVERT: d 7 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6522 (tt) outliers start: 128 outliers final: 59 residues processed: 128 average time/residue: 0.1538 time to fit residues: 22.0573 Evaluate side-chains 105 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 7 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 5 LEU 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 7 LEU Chi-restraints excluded: chain D residue 1 LEU Chi-restraints excluded: chain D residue 4 HIS Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain E residue 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 5 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 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 2 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 7 LEU 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 5 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 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 1 LEU 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 X residue 6 ARG 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 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 7 LEU Chi-restraints excluded: chain c residue 2 HIS Chi-restraints excluded: chain c residue 4 HIS Chi-restraints excluded: chain d residue 2 HIS Chi-restraints excluded: chain d residue 4 HIS Chi-restraints excluded: chain d residue 7 LEU 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** ** 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 0.8240 moved from start: 1.3563 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= 3.898 Angle : 5.863 32.771 2730 Z= 2.707 Chirality : 0.410 1.303 330 Planarity : 0.050 0.205 330 Dihedral : 10.368 33.656 270 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 298.96 Ramachandran Plot: Outliers : 45.33 % Allowed : 50.67 % Favored : 4.00 % Rotamer: Outliers : 65.24 % Allowed : 14.76 % Favored : 20.00 % Cbeta Deviations : 11.90 % 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 0.052 0.013 HIS S 4 ARG 0.014 0.002 ARG F 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 137 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 0 time to evaluate : 0.263 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: 0.7793 (t-170) REVERT: A 5 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7862 (tt) REVERT: A 7 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8009 (tt) REVERT: B 2 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.7575 (t-170) REVERT: B 5 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7848 (tt) REVERT: B 7 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8048 (tt) REVERT: C 2 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7316 (t-170) REVERT: C 4 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.7457 (m90) REVERT: D 2 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.6603 (t-170) REVERT: E 2 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7833 (t-170) REVERT: F 2 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7857 (t-170) REVERT: F 7 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6601 (tt) REVERT: G 5 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8154 (tt) REVERT: H 5 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8281 (tt) REVERT: H 7 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8436 (tt) REVERT: I 4 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8317 (t70) REVERT: I 7 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8230 (tt) REVERT: J 7 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8285 (tt) REVERT: K 5 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8808 (tt) REVERT: L 7 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7234 (tt) REVERT: M 2 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8262 (t-170) REVERT: M 4 HIS cc_start: 0.9089 (OUTLIER) cc_final: 0.7938 (t70) REVERT: M 5 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8674 (tt) REVERT: N 2 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8256 (t-170) REVERT: N 4 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.7934 (t70) REVERT: N 5 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8653 (tt) REVERT: O 2 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8640 (t-170) REVERT: P 2 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8120 (t-170) REVERT: P 4 HIS cc_start: 0.9366 (OUTLIER) cc_final: 0.8366 (t70) REVERT: P 7 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8405 (tt) REVERT: Q 5 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9057 (tt) REVERT: R 5 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8946 (tt) REVERT: S 6 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8253 (ttt-90) REVERT: X 6 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8056 (tmt-80) REVERT: Y 2 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.7852 (t70) REVERT: Y 7 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8164 (tt) REVERT: Z 7 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (tt) REVERT: a 4 HIS cc_start: 0.8632 (OUTLIER) cc_final: 0.7900 (t70) REVERT: a 7 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7694 (tt) REVERT: b 4 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7692 (t70) REVERT: b 7 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7801 (tt) REVERT: d 5 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8220 (tt) outliers start: 137 outliers final: 73 residues processed: 137 average time/residue: 0.1772 time to fit residues: 26.8543 Evaluate side-chains 115 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 0 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 5 LEU 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 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 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain F residue 2 HIS Chi-restraints excluded: chain F residue 7 LEU 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 5 LEU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 7 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 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 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 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 1 LEU Chi-restraints excluded: chain V residue 4 HIS Chi-restraints excluded: chain W residue 1 LEU Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 5 LEU 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 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 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 5 LEU Chi-restraints excluded: chain d residue 6 ARG 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 0.8241 moved from start: 1.3688 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= 3.888 Angle : 5.877 32.930 2730 Z= 2.721 Chirality : 0.413 1.301 330 Planarity : 0.051 0.197 330 Dihedral : 10.365 33.404 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 297.46 Ramachandran Plot: Outliers : 46.00 % Allowed : 50.00 % Favored : 4.00 % Rotamer: Outliers : 67.62 % Allowed : 13.81 % Favored : 18.57 % 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: -10.75 (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 S 4 ARG 0.009 0.002 ARG Q 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 142 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 0 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7799 (t-170) REVERT: A 5 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7764 (tt) REVERT: A 7 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8006 (tt) REVERT: B 2 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7521 (t-170) REVERT: B 5 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 7 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8061 (tt) REVERT: C 2 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7333 (t-170) REVERT: C 4 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7494 (m90) REVERT: D 2 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.6691 (t-170) REVERT: E 2 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7812 (t-170) REVERT: E 7 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6656 (tt) REVERT: F 2 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7945 (t-170) REVERT: G 5 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8066 (tt) REVERT: G 7 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8433 (tt) REVERT: H 4 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.8166 (t70) REVERT: H 5 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8348 (tt) REVERT: H 6 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8229 (tmt-80) REVERT: H 7 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8465 (tt) REVERT: I 4 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8332 (t70) REVERT: I 7 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8265 (tt) REVERT: J 7 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8303 (tt) REVERT: K 4 HIS cc_start: 0.9063 (OUTLIER) cc_final: 0.8492 (t70) REVERT: L 7 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6937 (tt) REVERT: M 2 HIS cc_start: 0.9204 (OUTLIER) cc_final: 0.8273 (t-170) REVERT: M 4 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.7950 (t70) REVERT: M 5 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8670 (tt) REVERT: N 2 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8260 (t-170) REVERT: N 4 HIS cc_start: 0.9075 (OUTLIER) cc_final: 0.7941 (t70) REVERT: N 5 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (tt) REVERT: O 2 HIS cc_start: 0.9054 (OUTLIER) cc_final: 0.8649 (t-170) REVERT: P 2 HIS cc_start: 0.8919 (OUTLIER) cc_final: 0.8483 (t-170) REVERT: P 7 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8365 (tt) REVERT: Q 5 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9089 (tt) REVERT: S 6 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8248 (ttt-90) REVERT: Y 2 HIS cc_start: 0.8486 (OUTLIER) cc_final: 0.7874 (t70) REVERT: Y 7 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8145 (tt) REVERT: Z 7 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8111 (tt) REVERT: a 4 HIS cc_start: 0.8710 (OUTLIER) cc_final: 0.8026 (t70) REVERT: a 7 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7683 (tt) REVERT: b 4 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.7757 (t70) REVERT: b 7 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7843 (tt) outliers start: 142 outliers final: 77 residues processed: 142 average time/residue: 0.2199 time to fit residues: 34.2954 Evaluate side-chains 122 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 4 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 5 LEU 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 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 1 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 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 H residue 6 ARG Chi-restraints excluded: chain H residue 7 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 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 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 1 LEU Chi-restraints excluded: chain W residue 2 HIS Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU 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 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 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 1 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=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** ** 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 0.8240 moved from start: 1.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.287 2040 Z= 3.884 Angle : 5.893 32.866 2730 Z= 2.729 Chirality : 0.415 1.306 330 Planarity : 0.050 0.197 330 Dihedral : 10.462 33.954 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 301.09 Ramachandran Plot: Outliers : 43.33 % Allowed : 52.67 % Favored : 4.00 % Rotamer: Outliers : 62.86 % Allowed : 16.19 % Favored : 20.95 % 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 0.054 0.013 HIS S 4 ARG 0.011 0.002 ARG F 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 132 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 0 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.7793 (t-170) REVERT: A 5 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 7 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8086 (tt) REVERT: B 2 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7507 (t-170) REVERT: B 5 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 7 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8135 (tt) REVERT: C 2 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7363 (t-170) REVERT: C 4 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7456 (m90) REVERT: C 5 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8208 (tt) REVERT: D 2 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.6721 (t-170) REVERT: E 2 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7903 (t-170) REVERT: F 2 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7934 (t-170) REVERT: G 5 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8090 (tt) REVERT: G 7 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8460 (tt) REVERT: H 4 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.8169 (t70) REVERT: H 5 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8297 (tt) REVERT: H 6 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8221 (tmt-80) REVERT: I 4 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8269 (t70) REVERT: I 7 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (tt) REVERT: J 4 HIS cc_start: 0.8941 (OUTLIER) cc_final: 0.8451 (t70) REVERT: J 7 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8203 (tt) REVERT: K 4 HIS cc_start: 0.9025 (OUTLIER) cc_final: 0.8447 (t70) REVERT: K 7 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6752 (tt) REVERT: L 7 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7065 (tt) REVERT: M 2 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8277 (t-170) REVERT: M 4 HIS cc_start: 0.9080 (OUTLIER) cc_final: 0.7953 (t70) REVERT: M 5 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8678 (tt) REVERT: N 2 HIS cc_start: 0.9178 (OUTLIER) cc_final: 0.8276 (t-170) REVERT: N 4 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.7947 (t70) REVERT: N 5 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8656 (tt) REVERT: O 2 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8624 (t-170) REVERT: P 2 HIS cc_start: 0.8954 (OUTLIER) cc_final: 0.8503 (t-170) REVERT: P 7 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8334 (tt) REVERT: R 7 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7439 (tt) REVERT: S 6 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8252 (ttt-90) REVERT: X 6 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7923 (tmt-80) REVERT: Y 2 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.7869 (t70) REVERT: Y 7 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8188 (tt) REVERT: Z 7 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (tt) REVERT: a 4 HIS cc_start: 0.8713 (OUTLIER) cc_final: 0.8006 (t70) REVERT: a 7 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7686 (tt) REVERT: b 4 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.7897 (t70) REVERT: b 7 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7822 (tt) outliers start: 132 outliers final: 76 residues processed: 132 average time/residue: 0.1888 time to fit residues: 27.5179 Evaluate side-chains 121 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 2 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 5 LEU 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 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 1 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 H residue 6 ARG 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 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 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 6 ARG 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 R 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 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 1 LEU Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU 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 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 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 1 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=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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 0.8241 moved from start: 1.3877 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= 3.871 Angle : 5.892 33.000 2730 Z= 2.730 Chirality : 0.414 1.303 330 Planarity : 0.050 0.193 330 Dihedral : 10.566 34.425 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 300.14 Ramachandran Plot: Outliers : 45.33 % Allowed : 50.67 % Favored : 4.00 % Rotamer: Outliers : 62.86 % Allowed : 15.24 % Favored : 21.90 % 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 : -8.18 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.013 HIS S 4 ARG 0.010 0.002 ARG R 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 132 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 0 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7808 (t-170) REVERT: A 5 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 7 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 2 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7518 (t-170) REVERT: B 5 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7773 (tt) REVERT: B 7 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8137 (tt) REVERT: C 2 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7388 (t-170) REVERT: C 4 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7466 (m90) REVERT: C 5 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8194 (tt) REVERT: D 2 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.6677 (t-170) REVERT: E 2 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7902 (t-170) REVERT: E 6 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7972 (ttt-90) REVERT: F 4 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8198 (m90) REVERT: F 6 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8088 (tmt170) REVERT: F 7 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6377 (tt) REVERT: G 5 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (tt) REVERT: G 7 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8378 (tt) REVERT: H 4 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8195 (t70) REVERT: H 5 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8298 (tt) REVERT: H 6 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8205 (tmt-80) REVERT: I 4 HIS cc_start: 0.8911 (OUTLIER) cc_final: 0.8250 (t70) REVERT: I 7 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8163 (tt) REVERT: J 6 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8564 (ttt180) REVERT: J 7 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8162 (tt) REVERT: K 4 HIS cc_start: 0.9023 (OUTLIER) cc_final: 0.8350 (t70) REVERT: L 5 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8811 (tt) REVERT: L 7 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7201 (tt) REVERT: M 2 HIS cc_start: 0.9218 (OUTLIER) cc_final: 0.8295 (t-170) REVERT: M 4 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.7947 (t70) REVERT: M 5 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8671 (tt) REVERT: M 7 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8650 (tt) REVERT: N 2 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8307 (t-170) REVERT: N 4 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.7936 (t70) REVERT: N 5 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8662 (tt) REVERT: O 2 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8612 (t-170) REVERT: P 2 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8465 (t-170) REVERT: P 7 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8401 (tt) REVERT: R 7 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7338 (tt) REVERT: S 6 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8288 (ttt-90) REVERT: Y 2 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7924 (t70) REVERT: Y 7 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8206 (tt) REVERT: Z 7 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8114 (tt) REVERT: a 4 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.7953 (t70) REVERT: a 7 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7714 (tt) REVERT: b 4 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.7922 (t70) REVERT: b 7 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7879 (tt) outliers start: 132 outliers final: 75 residues processed: 132 average time/residue: 0.1881 time to fit residues: 27.1576 Evaluate side-chains 121 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 0 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 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 5 LEU 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 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 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 7 LEU 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 H residue 6 ARG 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 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 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 M residue 7 LEU 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 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R 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 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 1 LEU Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain X residue 1 LEU 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 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 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 1 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=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 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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: 0.8242 moved from start: 1.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.288 2040 Z= 3.870 Angle : 5.892 32.974 2730 Z= 2.731 Chirality : 0.412 1.304 330 Planarity : 0.050 0.194 330 Dihedral : 10.539 34.822 270 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 303.15 Ramachandran Plot: Outliers : 44.00 % Allowed : 52.00 % Favored : 4.00 % Rotamer: Outliers : 62.86 % Allowed : 18.10 % Favored : 19.05 % Cbeta Deviations : 10.95 % 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 0.053 0.013 HIS S 4 ARG 0.013 0.002 ARG R 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 132 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 0 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7791 (t-170) REVERT: A 5 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7762 (tt) REVERT: A 7 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8000 (tt) REVERT: B 2 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7518 (t-170) REVERT: B 5 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 7 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8104 (tt) REVERT: C 2 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7400 (t-170) REVERT: C 4 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7455 (m90) REVERT: C 5 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8169 (tt) REVERT: D 2 HIS cc_start: 0.7967 (OUTLIER) cc_final: 0.6690 (t-170) REVERT: E 2 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7942 (t-170) REVERT: E 6 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8050 (ttt-90) REVERT: F 6 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8065 (tmt170) REVERT: F 7 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6342 (tt) REVERT: G 5 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8096 (tt) REVERT: G 7 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8371 (tt) REVERT: H 4 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.8186 (t70) REVERT: H 5 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (tt) REVERT: H 6 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8151 (tmt-80) REVERT: I 4 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8255 (t70) REVERT: I 7 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8158 (tt) REVERT: J 6 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8558 (ttt180) REVERT: J 7 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8208 (tt) REVERT: K 4 HIS cc_start: 0.9017 (OUTLIER) cc_final: 0.8424 (t70) REVERT: K 7 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7170 (tt) REVERT: L 7 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7090 (tt) REVERT: M 2 HIS cc_start: 0.9206 (OUTLIER) cc_final: 0.8266 (t-170) REVERT: M 4 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.7940 (t70) REVERT: M 5 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8674 (tt) REVERT: M 7 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8646 (tt) REVERT: N 2 HIS cc_start: 0.9169 (OUTLIER) cc_final: 0.8268 (t-170) REVERT: N 4 HIS cc_start: 0.9062 (OUTLIER) cc_final: 0.7945 (t70) REVERT: N 5 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8642 (tt) REVERT: O 2 HIS cc_start: 0.9018 (OUTLIER) cc_final: 0.8577 (t-170) REVERT: P 2 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8480 (t-170) REVERT: P 7 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8418 (tt) REVERT: R 7 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7209 (tt) REVERT: S 6 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8278 (ttt-90) REVERT: W 6 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.7923 (ttt-90) REVERT: X 6 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8012 (tmt-80) REVERT: X 7 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7592 (tt) REVERT: Y 2 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.7885 (t70) REVERT: Y 7 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8234 (tt) REVERT: Z 7 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8070 (tt) REVERT: a 4 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.7907 (t70) REVERT: a 7 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7728 (tt) REVERT: b 4 HIS cc_start: 0.8672 (OUTLIER) cc_final: 0.7991 (t70) REVERT: b 7 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7766 (tt) outliers start: 132 outliers final: 75 residues processed: 132 average time/residue: 0.2156 time to fit residues: 31.1806 Evaluate side-chains 124 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 5 LEU 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 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 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 7 LEU 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 H residue 6 ARG 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 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 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 M residue 7 LEU 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 6 ARG Chi-restraints excluded: chain R residue 2 HIS Chi-restraints excluded: chain R residue 4 HIS Chi-restraints excluded: chain R 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 4 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 1 LEU Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 1 LEU 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 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 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 1 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=1.50 ------------------------------------------------------------------------------- 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 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 1.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.289 2040 Z= 3.874 Angle : 5.886 32.928 2730 Z= 2.733 Chirality : 0.413 1.309 330 Planarity : 0.050 0.195 330 Dihedral : 10.561 34.775 270 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 304.57 Ramachandran Plot: Outliers : 43.33 % Allowed : 52.67 % Favored : 4.00 % Rotamer: Outliers : 61.43 % Allowed : 18.10 % Favored : 20.48 % Cbeta Deviations : 10.95 % 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 0.054 0.014 HIS S 4 ARG 0.017 0.002 ARG R 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 129 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 0 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7795 (t-170) REVERT: A 5 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7758 (tt) REVERT: A 7 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7999 (tt) REVERT: B 2 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7539 (t-170) REVERT: B 5 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7762 (tt) REVERT: B 7 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8198 (tt) REVERT: C 2 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7391 (t-170) REVERT: C 4 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.7466 (m90) REVERT: C 5 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 2 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.6679 (t-170) REVERT: E 2 HIS cc_start: 0.8325 (OUTLIER) cc_final: 0.7954 (t-170) REVERT: E 6 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7941 (ttt-90) REVERT: F 4 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.8162 (m90) REVERT: F 6 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.8045 (tmt170) REVERT: F 7 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6395 (tt) REVERT: G 5 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8104 (tt) REVERT: G 7 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8439 (tt) REVERT: H 4 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.8197 (t70) REVERT: H 5 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8299 (tt) REVERT: H 6 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8124 (tmt-80) REVERT: I 4 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8234 (t70) REVERT: I 7 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8129 (tt) REVERT: J 6 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8548 (ttt180) REVERT: J 7 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8292 (tt) REVERT: K 4 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8304 (t70) REVERT: K 7 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7105 (tt) REVERT: L 7 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6934 (tt) REVERT: M 2 HIS cc_start: 0.9216 (OUTLIER) cc_final: 0.8290 (t-170) REVERT: M 4 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.7926 (t70) REVERT: M 5 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8668 (tt) REVERT: M 7 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8666 (tt) REVERT: N 2 HIS cc_start: 0.9171 (OUTLIER) cc_final: 0.8256 (t-170) REVERT: N 4 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.7942 (t70) REVERT: N 5 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8649 (tt) REVERT: O 2 HIS cc_start: 0.9015 (OUTLIER) cc_final: 0.8597 (t-170) REVERT: P 2 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8543 (t-170) REVERT: R 5 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9061 (tt) REVERT: S 6 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8318 (ttt-90) REVERT: W 6 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7983 (ttt-90) REVERT: X 7 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7488 (tt) REVERT: Y 2 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.7896 (t70) REVERT: Z 2 HIS cc_start: 0.8506 (OUTLIER) cc_final: 0.8038 (t70) REVERT: Z 7 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8064 (tt) REVERT: a 4 HIS cc_start: 0.8649 (OUTLIER) cc_final: 0.7965 (t70) REVERT: a 7 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7679 (tt) REVERT: b 4 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8005 (t70) REVERT: b 7 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7822 (tt) outliers start: 129 outliers final: 77 residues processed: 129 average time/residue: 0.2038 time to fit residues: 28.7347 Evaluate side-chains 125 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 5 LEU 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 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 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 7 LEU 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 H residue 6 ARG 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 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 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 M residue 7 LEU 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 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 S residue 1 LEU Chi-restraints excluded: chain S residue 2 HIS Chi-restraints excluded: chain S residue 4 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 1 LEU Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 1 LEU 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 2 HIS Chi-restraints excluded: chain Y residue 6 ARG Chi-restraints excluded: chain Z residue 1 LEU Chi-restraints excluded: chain Z residue 2 HIS 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 1 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 2 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 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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 2 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 1.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.287 2040 Z= 3.876 Angle : 5.901 32.937 2730 Z= 2.740 Chirality : 0.415 1.305 330 Planarity : 0.050 0.196 330 Dihedral : 10.729 34.903 270 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 306.00 Ramachandran Plot: Outliers : 44.00 % Allowed : 52.00 % Favored : 4.00 % Rotamer: Outliers : 60.95 % Allowed : 17.14 % Favored : 21.90 % Cbeta Deviations : 10.95 % 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 0.054 0.013 HIS S 4 ARG 0.010 0.002 ARG R 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 128 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 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: 0.8362 (OUTLIER) cc_final: 0.7800 (t-170) REVERT: A 5 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 7 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7978 (tt) REVERT: B 2 HIS cc_start: 0.8374 (OUTLIER) cc_final: 0.7532 (t-170) REVERT: B 5 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7761 (tt) REVERT: B 7 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8163 (tt) REVERT: C 2 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7384 (t-170) REVERT: C 4 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.7494 (m90) REVERT: C 5 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8131 (tt) REVERT: D 2 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.6672 (t-170) REVERT: E 2 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7969 (t-170) REVERT: E 6 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8045 (ttt-90) REVERT: F 5 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8299 (tt) REVERT: G 5 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8100 (tt) REVERT: G 7 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8442 (tt) REVERT: H 4 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.8196 (t70) REVERT: H 5 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8306 (tt) REVERT: H 6 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8115 (tmt-80) REVERT: I 4 HIS cc_start: 0.8940 (OUTLIER) cc_final: 0.8235 (t70) REVERT: I 7 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8145 (tt) REVERT: J 4 HIS cc_start: 0.8980 (OUTLIER) cc_final: 0.8485 (t70) REVERT: J 7 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8325 (tt) REVERT: K 4 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8308 (t70) REVERT: K 7 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7100 (tt) REVERT: L 7 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6932 (tt) REVERT: M 2 HIS cc_start: 0.9222 (OUTLIER) cc_final: 0.8288 (t-170) REVERT: M 4 HIS cc_start: 0.9090 (OUTLIER) cc_final: 0.7954 (t70) REVERT: M 5 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8667 (tt) REVERT: N 2 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8252 (t-170) REVERT: N 4 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.7942 (t70) REVERT: N 5 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8649 (tt) REVERT: O 2 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8619 (t-170) REVERT: P 2 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8532 (t-170) REVERT: R 5 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8997 (tt) REVERT: S 6 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8309 (ttt-90) REVERT: W 6 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7934 (ttt-90) REVERT: X 6 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7967 (tmt-80) REVERT: Y 2 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.7889 (t70) REVERT: Z 7 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8095 (tt) REVERT: a 4 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.7988 (t70) REVERT: a 7 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7749 (tt) REVERT: b 4 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.8052 (t70) REVERT: b 7 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7784 (tt) outliers start: 128 outliers final: 76 residues processed: 128 average time/residue: 0.2021 time to fit residues: 28.2848 Evaluate side-chains 122 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 3 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 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 5 LEU 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 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 1 LEU Chi-restraints excluded: chain E residue 2 HIS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain F residue 4 HIS Chi-restraints excluded: chain F residue 5 LEU 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 H residue 6 ARG 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 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 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 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 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 1 LEU Chi-restraints excluded: chain W residue 4 HIS Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain X residue 1 LEU 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 2 HIS Chi-restraints excluded: chain Y residue 6 ARG 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 1 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 2 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 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** ** S 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.083891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.069193 restraints weight = 6434.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.070651 restraints weight = 4312.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.071778 restraints weight = 3196.727| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 1.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.292 2040 Z= 3.874 Angle : 5.943 32.920 2730 Z= 2.752 Chirality : 0.417 1.305 330 Planarity : 0.049 0.195 330 Dihedral : 10.754 35.116 270 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 304.50 Ramachandran Plot: Outliers : 43.33 % Allowed : 52.00 % Favored : 4.67 % Rotamer: Outliers : 59.05 % Allowed : 15.71 % Favored : 25.24 % Cbeta Deviations : 11.90 % 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 0.053 0.013 HIS S 4 ARG 0.011 0.002 ARG R 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 875.15 seconds wall clock time: 21 minutes 16.58 seconds (1276.58 seconds total)