Starting phenix.real_space_refine on Sun Mar 10 18:38:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az7_15756/03_2024/8az7_15756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az7_15756/03_2024/8az7_15756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az7_15756/03_2024/8az7_15756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az7_15756/03_2024/8az7_15756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az7_15756/03_2024/8az7_15756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az7_15756/03_2024/8az7_15756_updated.pdb" } resolution = 2.9 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 2470 2.51 5 N 740 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 11": "NH1" <-> "NH2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 11": "NH1" <-> "NH2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 11": "NH1" <-> "NH2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 11": "NH1" <-> "NH2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4010 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "C" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "D" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "G" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "H" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "I" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "J" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "K" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "L" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "M" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "N" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "O" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "P" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "Q" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "R" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "S" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Chain: "T" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 183 Unusual residues: {'NH2': 1} Classifications: {'peptide': 25, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 24} Time building chain proxies: 2.48, per 1000 atoms: 0.62 Number of scatterers: 4010 At special positions: 0 Unit cell: (70.2, 89.1, 48.6, 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 800 8.00 N 740 7.00 C 2470 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: 1.41 Conformation dependent library (CDL) restraints added in 844.8 milliseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 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: 0.56 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: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 650 1.29 - 1.36: 740 1.36 - 1.42: 500 1.42 - 1.49: 600 1.49 - 1.55: 1580 Bond restraints: 4070 Sorted by residual: bond pdb=" N GLY C 20 " pdb=" CA GLY C 20 " ideal model delta sigma weight residual 1.442 1.455 -0.013 7.70e-03 1.69e+04 2.73e+00 bond pdb=" N GLY K 20 " pdb=" CA GLY K 20 " ideal model delta sigma weight residual 1.442 1.454 -0.013 7.70e-03 1.69e+04 2.69e+00 bond pdb=" N GLY H 20 " pdb=" CA GLY H 20 " ideal model delta sigma weight residual 1.442 1.454 -0.012 7.70e-03 1.69e+04 2.59e+00 bond pdb=" N GLY G 20 " pdb=" CA GLY G 20 " ideal model delta sigma weight residual 1.442 1.454 -0.012 7.70e-03 1.69e+04 2.49e+00 bond pdb=" N GLY L 20 " pdb=" CA GLY L 20 " ideal model delta sigma weight residual 1.442 1.454 -0.012 7.70e-03 1.69e+04 2.44e+00 ... (remaining 4065 not shown) Histogram of bond angle deviations from ideal: 106.09 - 111.11: 1739 111.11 - 116.14: 800 116.14 - 121.17: 1707 121.17 - 126.20: 1264 126.20 - 131.23: 20 Bond angle restraints: 5530 Sorted by residual: angle pdb=" C SER T 19 " pdb=" N GLY T 20 " pdb=" CA GLY T 20 " ideal model delta sigma weight residual 122.69 119.55 3.14 1.04e+00 9.25e-01 9.13e+00 angle pdb=" C SER S 19 " pdb=" N GLY S 20 " pdb=" CA GLY S 20 " ideal model delta sigma weight residual 122.69 119.55 3.14 1.04e+00 9.25e-01 9.12e+00 angle pdb=" C SER P 19 " pdb=" N GLY P 20 " pdb=" CA GLY P 20 " ideal model delta sigma weight residual 122.69 119.57 3.12 1.04e+00 9.25e-01 9.01e+00 angle pdb=" C SER O 19 " pdb=" N GLY O 20 " pdb=" CA GLY O 20 " ideal model delta sigma weight residual 122.69 119.59 3.10 1.04e+00 9.25e-01 8.89e+00 angle pdb=" N SER T 19 " pdb=" CA SER T 19 " pdb=" C SER T 19 " ideal model delta sigma weight residual 110.61 113.76 -3.15 1.25e+00 6.40e-01 6.34e+00 ... (remaining 5525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.85: 2071 10.85 - 21.69: 139 21.69 - 32.54: 30 32.54 - 43.38: 0 43.38 - 54.23: 10 Dihedral angle restraints: 2250 sinusoidal: 750 harmonic: 1500 Sorted by residual: dihedral pdb=" CA PHE S 23 " pdb=" CB PHE S 23 " pdb=" CG PHE S 23 " pdb=" CD1 PHE S 23 " ideal model delta sinusoidal sigma weight residual -20.00 34.23 -54.23 2 2.00e+01 2.50e-03 7.90e+00 dihedral pdb=" CA PHE T 23 " pdb=" CB PHE T 23 " pdb=" CG PHE T 23 " pdb=" CD1 PHE T 23 " ideal model delta sinusoidal sigma weight residual -20.00 34.18 -54.18 2 2.00e+01 2.50e-03 7.89e+00 dihedral pdb=" CA PHE O 23 " pdb=" CB PHE O 23 " pdb=" CG PHE O 23 " pdb=" CD1 PHE O 23 " ideal model delta sinusoidal sigma weight residual -20.00 34.03 -54.03 2 2.00e+01 2.50e-03 7.86e+00 ... (remaining 2247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 421 0.028 - 0.055: 148 0.055 - 0.083: 12 0.083 - 0.111: 29 0.111 - 0.138: 30 Chirality restraints: 640 Sorted by residual: chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE H 26 " pdb=" N ILE H 26 " pdb=" C ILE H 26 " pdb=" CB ILE H 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE K 26 " pdb=" N ILE K 26 " pdb=" C ILE K 26 " pdb=" CB ILE K 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 637 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 15 " -0.003 2.00e-02 2.50e+03 6.32e-03 6.99e-01 pdb=" CG PHE H 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE H 15 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 15 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE H 15 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 15 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 15 " -0.003 2.00e-02 2.50e+03 6.31e-03 6.96e-01 pdb=" CG PHE K 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE K 15 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE K 15 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE K 15 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 15 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 15 " -0.003 2.00e-02 2.50e+03 6.23e-03 6.78e-01 pdb=" CG PHE L 15 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE L 15 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE L 15 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE L 15 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE L 15 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE L 15 " -0.000 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.66 - 3.11: 2866 3.11 - 3.56: 4252 3.56 - 4.01: 6260 4.01 - 4.45: 7570 4.45 - 4.90: 12586 Nonbonded interactions: 33534 Sorted by model distance: nonbonded pdb=" O ASN I 22 " pdb=" N PHE M 23 " model vdw 2.665 2.520 nonbonded pdb=" O SER P 19 " pdb=" CB SER P 19 " model vdw 2.667 2.752 nonbonded pdb=" O SER S 19 " pdb=" CB SER S 19 " model vdw 2.667 2.752 nonbonded pdb=" O SER T 19 " pdb=" CB SER T 19 " model vdw 2.667 2.752 nonbonded pdb=" O SER O 19 " pdb=" CB SER O 19 " model vdw 2.667 2.752 ... (remaining 33529 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' and resid 13 through 38) selection = (chain 'B' and resid 13 through 38) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 13 through 38) selection = (chain 'F' and resid 13 through 38) selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 13 through 38) selection = (chain 'J' and resid 13 through 38) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 13 through 38) selection = (chain 'N' and resid 13 through 38) selection = chain 'O' selection = chain 'P' selection = (chain 'Q' and resid 13 through 38) selection = (chain 'R' and resid 13 through 38) selection = chain 'S' selection = chain 'T' } 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 individual isotropic 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: 1.350 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: 5.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.150 Find NCS groups from input model: 0.310 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.003 0.013 4070 Z= 0.144 Angle : 0.506 3.439 5530 Z= 0.341 Chirality : 0.042 0.138 640 Planarity : 0.001 0.006 740 Dihedral : 8.791 54.230 1290 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS S 18 PHE 0.013 0.002 PHE L 15 TYR 0.003 0.001 TYR Q 37 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.484 Fit side-chains REVERT: A 11 ARG cc_start: 0.7483 (mtp180) cc_final: 0.7256 (mmm160) REVERT: D 31 ASN cc_start: 0.8426 (t0) cc_final: 0.8222 (t0) REVERT: P 31 ASN cc_start: 0.8366 (t0) cc_final: 0.8155 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.7096 time to fit residues: 65.1222 Evaluate side-chains 78 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN C 14 ASN ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 ASN G 14 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN H 14 ASN ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN K 14 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN ** N 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN O 14 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN P 14 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 HIS Q 21 ASN ** R 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 ASN S 14 ASN ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 14 ASN ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 4070 Z= 0.311 Angle : 0.603 4.860 5530 Z= 0.347 Chirality : 0.046 0.145 640 Planarity : 0.003 0.020 740 Dihedral : 5.183 13.269 550 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.18 % Allowed : 5.68 % Favored : 91.14 % 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: -3.62 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 18 PHE 0.011 0.002 PHE E 15 TYR 0.012 0.002 TYR R 37 ARG 0.004 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.479 Fit side-chains REVERT: P 31 ASN cc_start: 0.8366 (t0) cc_final: 0.8141 (t0) outliers start: 14 outliers final: 2 residues processed: 97 average time/residue: 0.7273 time to fit residues: 74.1642 Evaluate side-chains 95 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN M 14 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN R 18 HIS T 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 4070 Z= 0.185 Angle : 0.566 7.003 5530 Z= 0.305 Chirality : 0.044 0.141 640 Planarity : 0.002 0.020 740 Dihedral : 4.873 13.063 550 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.59 % Allowed : 12.27 % Favored : 86.14 % 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: -3.64 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS N 18 PHE 0.008 0.001 PHE K 15 TYR 0.008 0.001 TYR S 37 ARG 0.004 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.459 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 95 average time/residue: 0.6913 time to fit residues: 69.1581 Evaluate side-chains 97 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain L residue 21 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 HIS ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN T 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4070 Z= 0.134 Angle : 0.518 6.777 5530 Z= 0.278 Chirality : 0.043 0.139 640 Planarity : 0.002 0.020 740 Dihedral : 4.530 12.245 550 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.36 % Allowed : 13.41 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.008 0.001 PHE L 15 TYR 0.009 0.001 TYR S 37 ARG 0.004 0.001 ARG F 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.415 Fit side-chains REVERT: A 11 ARG cc_start: 0.5621 (mmm160) cc_final: 0.5082 (mtp85) outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 0.7497 time to fit residues: 71.7243 Evaluate side-chains 92 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 18 HIS ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS F 18 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN I 18 HIS J 18 HIS ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4070 Z= 0.367 Angle : 0.696 7.504 5530 Z= 0.379 Chirality : 0.048 0.151 640 Planarity : 0.003 0.030 740 Dihedral : 5.501 14.617 550 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.59 % Allowed : 15.68 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 18 PHE 0.010 0.002 PHE K 15 TYR 0.010 0.002 TYR F 37 ARG 0.007 0.001 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 0.424 Fit side-chains REVERT: A 11 ARG cc_start: 0.5815 (mmm160) cc_final: 0.5454 (mmm160) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.6952 time to fit residues: 77.6385 Evaluate side-chains 106 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN T 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4070 Z= 0.180 Angle : 0.634 7.875 5530 Z= 0.321 Chirality : 0.045 0.159 640 Planarity : 0.002 0.029 740 Dihedral : 4.951 15.053 550 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.59 % Allowed : 18.18 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS S 18 PHE 0.007 0.001 PHE K 15 TYR 0.010 0.001 TYR S 37 ARG 0.007 0.001 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.408 Fit side-chains REVERT: A 11 ARG cc_start: 0.5925 (mmm160) cc_final: 0.5439 (mmm160) outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 0.7704 time to fit residues: 80.0227 Evaluate side-chains 98 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN M 14 ASN ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN T 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 4070 Z= 0.283 Angle : 0.690 7.793 5530 Z= 0.358 Chirality : 0.046 0.146 640 Planarity : 0.002 0.027 740 Dihedral : 5.263 15.191 550 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.27 % Allowed : 17.73 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 18 PHE 0.009 0.002 PHE K 15 TYR 0.010 0.001 TYR S 37 ARG 0.007 0.001 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.478 Fit side-chains REVERT: A 11 ARG cc_start: 0.5834 (mmm160) cc_final: 0.5006 (mtp85) outliers start: 10 outliers final: 4 residues processed: 96 average time/residue: 0.7200 time to fit residues: 72.8915 Evaluate side-chains 96 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN S 14 ASN T 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4070 Z= 0.200 Angle : 0.651 8.385 5530 Z= 0.334 Chirality : 0.045 0.143 640 Planarity : 0.002 0.031 740 Dihedral : 5.013 14.759 550 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.05 % Allowed : 18.18 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 18 PHE 0.007 0.001 PHE K 15 TYR 0.012 0.001 TYR S 37 ARG 0.007 0.001 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.466 Fit side-chains REVERT: A 11 ARG cc_start: 0.5823 (mmm160) cc_final: 0.5049 (mtp85) outliers start: 9 outliers final: 4 residues processed: 97 average time/residue: 0.7225 time to fit residues: 73.8130 Evaluate side-chains 97 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4070 Z= 0.291 Angle : 0.721 8.232 5530 Z= 0.369 Chirality : 0.047 0.147 640 Planarity : 0.003 0.032 740 Dihedral : 5.303 15.161 550 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.82 % Allowed : 18.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 18 PHE 0.007 0.002 PHE K 15 TYR 0.012 0.001 TYR S 37 ARG 0.008 0.001 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.447 Fit side-chains REVERT: A 11 ARG cc_start: 0.5816 (mmm160) cc_final: 0.5376 (mmm160) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 0.7193 time to fit residues: 72.7561 Evaluate side-chains 97 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN S 14 ASN T 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4070 Z= 0.191 Angle : 0.682 8.756 5530 Z= 0.340 Chirality : 0.045 0.142 640 Planarity : 0.002 0.034 740 Dihedral : 5.010 14.886 550 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.82 % Allowed : 18.64 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS S 18 PHE 0.006 0.001 PHE K 23 TYR 0.013 0.001 TYR S 37 ARG 0.008 0.001 ARG M 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.436 Fit side-chains REVERT: A 11 ARG cc_start: 0.5792 (mmm160) cc_final: 0.5012 (mtp85) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.6073 time to fit residues: 60.0293 Evaluate side-chains 96 residues out of total 440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 ASN Chi-restraints excluded: chain G residue 35 ASN Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN T 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.132127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.083575 restraints weight = 5370.674| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.52 r_work: 0.3089 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4070 Z= 0.238 Angle : 0.703 8.558 5530 Z= 0.353 Chirality : 0.046 0.145 640 Planarity : 0.003 0.032 740 Dihedral : 5.112 14.812 550 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.82 % Allowed : 18.41 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.22), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.17), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 18 PHE 0.006 0.001 PHE K 23 TYR 0.013 0.001 TYR S 37 ARG 0.009 0.001 ARG M 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.98 seconds wall clock time: 32 minutes 5.87 seconds (1925.87 seconds total)