Starting phenix.real_space_refine on Thu Dec 7 15:49:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/12_2023/8b3a_15824_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/12_2023/8b3a_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_15824/12_2023/8b3a_15824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/12_2023/8b3a_15824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/12_2023/8b3a_15824_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b3a_15824/12_2023/8b3a_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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2010 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "M" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "O" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "P" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "Q" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "R" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "S" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "T" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "V" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "X" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "Y" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "Z" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "a" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "b" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "c" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Chain: "d" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {'ACE': 1, 'NH2': 1} Classifications: {'peptide': 7, 'undetermined': 2} Link IDs: {'ACE_C-N': 1, 'NH2_CTERM': 1, 'TRANS': 6} Time building chain proxies: 1.20, per 1000 atoms: 0.60 Number of scatterers: 2010 At special positions: 0 Unit cell: (90.48, 49.92, 37.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 240 8.00 N 450 7.00 C 1320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 257.3 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.91 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: 0.340 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: 1.680 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.180 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.980 ------------------------------------------------------------------------------- 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 : 0.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.8679 time to fit residues: 2.1617 Evaluate side-chains 0 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 0 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3239 ------------------------------------------------------------------------------- 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 : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 39 residues processed: 103 average time/residue: 0.1225 time to fit residues: 14.5819 Evaluate side-chains 50 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 11 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.0364 time to fit residues: 2.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** b 2 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: 0.8234 moved from start: 1.3691 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 : 6.004 33.234 2730 Z= 2.751 Chirality : 0.409 1.325 330 Planarity : 0.051 0.178 330 Dihedral : 11.209 33.948 270 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 302.35 Ramachandran Plot: Outliers : 48.00 % Allowed : 47.33 % Favored : 4.67 % Rotamer: Outliers : 59.05 % Allowed : 20.00 % Favored : 20.95 % Cbeta Deviations : 14.29 % 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 : -8.19 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.053 0.013 HIS D 4 ARG 0.009 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 124 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 0 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 67 residues processed: 124 average time/residue: 0.1692 time to fit residues: 23.3387 Evaluate side-chains 81 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 14 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.0999 time to fit residues: 8.0578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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 2 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8234 moved from start: 1.4098 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= 3.874 Angle : 5.994 33.408 2730 Z= 2.789 Chirality : 0.413 1.328 330 Planarity : 0.051 0.194 330 Dihedral : 11.294 35.645 270 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 302.11 Ramachandran Plot: Outliers : 49.33 % Allowed : 44.67 % Favored : 6.00 % Rotamer: Outliers : 49.05 % Allowed : 24.76 % Favored : 26.19 % Cbeta Deviations : 12.38 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.052 0.013 HIS S 4 ARG 0.015 0.002 ARG H 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 0 time to evaluate : 0.264 Fit side-chains outliers start: 103 outliers final: 54 residues processed: 103 average time/residue: 0.1669 time to fit residues: 19.2521 Evaluate side-chains 62 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 8 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.0850 time to fit residues: 5.7686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8225 moved from start: 1.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.287 2040 Z= 3.829 Angle : 5.995 33.897 2730 Z= 2.791 Chirality : 0.413 1.348 330 Planarity : 0.051 0.198 330 Dihedral : 11.519 38.317 270 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 300.92 Ramachandran Plot: Outliers : 45.33 % Allowed : 48.00 % Favored : 6.67 % Rotamer: Outliers : 51.90 % Allowed : 23.81 % Favored : 24.29 % Cbeta Deviations : 12.38 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.054 0.012 HIS S 4 ARG 0.013 0.002 ARG d 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 109 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 0 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 53 residues processed: 109 average time/residue: 0.1747 time to fit residues: 21.1554 Evaluate side-chains 69 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 16 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.0698 time to fit residues: 4.8434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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 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 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8225 moved from start: 1.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.283 2040 Z= 3.796 Angle : 6.083 34.605 2730 Z= 2.833 Chirality : 0.416 1.366 330 Planarity : 0.049 0.194 330 Dihedral : 11.487 40.303 270 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 310.50 Ramachandran Plot: Outliers : 46.67 % Allowed : 46.00 % Favored : 7.33 % Rotamer: Outliers : 42.38 % Allowed : 29.05 % Favored : 28.57 % Cbeta Deviations : 13.81 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.051 0.012 HIS S 4 ARG 0.017 0.002 ARG S 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 89 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 0 time to evaluate : 0.272 Fit side-chains outliers start: 89 outliers final: 41 residues processed: 89 average time/residue: 0.1267 time to fit residues: 13.1218 Evaluate side-chains 46 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 5 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.0574 time to fit residues: 3.3256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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 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 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8228 moved from start: 1.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 0.282 2040 Z= 3.782 Angle : 6.199 35.997 2730 Z= 2.860 Chirality : 0.422 1.405 330 Planarity : 0.051 0.201 330 Dihedral : 11.635 42.228 270 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 310.17 Ramachandran Plot: Outliers : 46.67 % Allowed : 46.00 % Favored : 7.33 % Rotamer: Outliers : 34.76 % Allowed : 36.19 % Favored : 29.05 % Cbeta Deviations : 13.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.059 0.013 HIS Y 2 ARG 0.012 0.002 ARG S 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 73 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 0 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 42 residues processed: 73 average time/residue: 0.1659 time to fit residues: 13.5305 Evaluate side-chains 44 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 2 time to evaluate : 0.191 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1157 time to fit residues: 5.8849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 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** ** I 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8226 moved from start: 1.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 0.284 2040 Z= 3.770 Angle : 6.278 36.864 2730 Z= 2.905 Chirality : 0.420 1.425 330 Planarity : 0.048 0.203 330 Dihedral : 11.514 43.764 270 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 317.22 Ramachandran Plot: Outliers : 46.67 % Allowed : 46.00 % Favored : 7.33 % Rotamer: Outliers : 26.19 % Allowed : 42.38 % Favored : 31.43 % Cbeta Deviations : 13.81 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -10.73 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.075 0.013 HIS Y 2 ARG 0.036 0.003 ARG S 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 55 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 0 time to evaluate : 0.275 Fit side-chains outliers start: 55 outliers final: 22 residues processed: 55 average time/residue: 0.1639 time to fit residues: 10.2756 Evaluate side-chains 30 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 8 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0628 time to fit residues: 2.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 1.9990 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8225 moved from start: 1.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.077 0.280 2040 Z= 3.761 Angle : 6.350 35.948 2730 Z= 2.939 Chirality : 0.430 1.428 330 Planarity : 0.049 0.204 330 Dihedral : 11.769 44.252 270 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 310.19 Ramachandran Plot: Outliers : 44.00 % Allowed : 48.67 % Favored : 7.33 % Rotamer: Outliers : 17.14 % Allowed : 47.14 % Favored : 35.71 % Cbeta Deviations : 15.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -10.72 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.07), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.097 0.014 HIS Y 2 ARG 0.016 0.003 ARG Z 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 36 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 0 time to evaluate : 0.275 Fit side-chains outliers start: 36 outliers final: 21 residues processed: 36 average time/residue: 0.0936 time to fit residues: 4.3586 Evaluate side-chains 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 4 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0277 time to fit residues: 1.2417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 1.9990 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** ** 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** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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: 0.8221 moved from start: 1.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.282 2040 Z= 3.754 Angle : 6.418 36.866 2730 Z= 2.972 Chirality : 0.431 1.724 330 Planarity : 0.049 0.202 330 Dihedral : 11.769 44.226 270 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 310.43 Ramachandran Plot: Outliers : 43.33 % Allowed : 48.67 % Favored : 8.00 % Rotamer: Outliers : 11.90 % Allowed : 49.52 % Favored : 38.57 % Cbeta Deviations : 14.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % 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: -10.72 (0.09), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.104 0.015 HIS Y 2 ARG 0.011 0.002 ARG A 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 25 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 0 time to evaluate : 0.266 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 25 average time/residue: 0.1997 time to fit residues: 5.8027 Evaluate side-chains 15 residues out of total 210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 3 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1121 time to fit residues: 1.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 1.9990 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** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 2 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** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 4 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 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 2 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 = 0.4272 r_free = 0.4272 target = 0.083412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.070090 restraints weight = 6824.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.071036 restraints weight = 4746.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.071992 restraints weight = 3769.265| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 1.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.078 0.286 2040 Z= 3.759 Angle : 6.433 37.340 2730 Z= 2.967 Chirality : 0.431 1.436 330 Planarity : 0.050 0.201 330 Dihedral : 12.016 43.800 270 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 313.51 Ramachandran Plot: Outliers : 44.67 % Allowed : 47.33 % Favored : 8.00 % Rotamer: Outliers : 3.81 % Allowed : 55.71 % Favored : 40.48 % Cbeta Deviations : 13.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.78 % 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: -10.72 (0.08), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -8.17 (0.06), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.103 0.015 HIS Y 2 ARG 0.033 0.003 ARG K 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 818.51 seconds wall clock time: 21 minutes 5.06 seconds (1265.06 seconds total)