Starting phenix.real_space_refine on Fri Apr 5 12:02:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/04_2024/8ikb_35508_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/04_2024/8ikb_35508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/04_2024/8ikb_35508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/04_2024/8ikb_35508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/04_2024/8ikb_35508_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/04_2024/8ikb_35508_updated.pdb" } resolution = 3.71 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: 4 Type Number sf(0) Gaussians I 28 10.91 5 C 1064 2.51 5 N 308 2.21 5 O 364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 1764 Number of models: 1 Model: "" Number of chains: 28 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 63 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHI:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.03, per 1000 atoms: 0.58 Number of scatterers: 1764 At special positions: 0 Unit cell: (141.93, 97.94, 27.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) I 28 52.95 O 364 8.00 N 308 7.00 C 1064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 208.0 milliseconds 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 280 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: 0.26 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: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 975 1.39 - 1.57: 789 1.57 - 1.74: 0 1.74 - 1.92: 0 1.92 - 2.09: 28 Bond restraints: 1792 Sorted by residual: bond pdb=" CZ PHI i 216 " pdb=" I PHI i 216 " ideal model delta sigma weight residual 2.106 2.004 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" CZ PHI Z 216 " pdb=" I PHI Z 216 " ideal model delta sigma weight residual 2.106 2.009 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" CZ PHI D 216 " pdb=" I PHI D 216 " ideal model delta sigma weight residual 2.106 2.010 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CZ PHI j 216 " pdb=" I PHI j 216 " ideal model delta sigma weight residual 2.106 2.014 0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" CZ PHI a 216 " pdb=" I PHI a 216 " ideal model delta sigma weight residual 2.106 2.018 0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 1787 not shown) Histogram of bond angle deviations from ideal: 83.65 - 98.18: 54 98.18 - 112.71: 405 112.71 - 127.24: 1876 127.24 - 141.77: 14 141.77 - 156.30: 3 Bond angle restraints: 2352 Sorted by residual: angle pdb=" N GLY W 218 " pdb=" CA GLY W 218 " pdb=" C GLY W 218 " ideal model delta sigma weight residual 115.32 142.71 -27.39 1.31e+00 5.83e-01 4.37e+02 angle pdb=" N PHE 3 222 " pdb=" CA PHE 3 222 " pdb=" C PHE 3 222 " ideal model delta sigma weight residual 111.69 88.32 23.37 1.23e+00 6.61e-01 3.61e+02 angle pdb=" N GLY q 218 " pdb=" CA GLY q 218 " pdb=" C GLY q 218 " ideal model delta sigma weight residual 112.64 135.05 -22.41 1.21e+00 6.83e-01 3.43e+02 angle pdb=" N ASN P 221 " pdb=" CA ASN P 221 " pdb=" C ASN P 221 " ideal model delta sigma weight residual 111.07 129.26 -18.19 1.07e+00 8.73e-01 2.89e+02 angle pdb=" N PHE e 222 " pdb=" CA PHE e 222 " pdb=" C PHE e 222 " ideal model delta sigma weight residual 113.55 93.47 20.08 1.26e+00 6.30e-01 2.54e+02 ... (remaining 2347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 678 15.23 - 30.46: 62 30.46 - 45.68: 12 45.68 - 60.91: 2 60.91 - 76.13: 2 Dihedral angle restraints: 756 sinusoidal: 252 harmonic: 504 Sorted by residual: dihedral pdb=" C ASN F 221 " pdb=" N ASN F 221 " pdb=" CA ASN F 221 " pdb=" CB ASN F 221 " ideal model delta harmonic sigma weight residual -122.60 -157.42 34.82 0 2.50e+00 1.60e-01 1.94e+02 dihedral pdb=" N ASN F 221 " pdb=" C ASN F 221 " pdb=" CA ASN F 221 " pdb=" CB ASN F 221 " ideal model delta harmonic sigma weight residual 122.80 157.23 -34.43 0 2.50e+00 1.60e-01 1.90e+02 dihedral pdb=" C PHI a 216 " pdb=" N PHI a 216 " pdb=" CA PHI a 216 " pdb=" CB PHI a 216 " ideal model delta harmonic sigma weight residual -122.60 -88.43 -34.17 0 2.50e+00 1.60e-01 1.87e+02 ... (remaining 753 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.321: 111 0.321 - 0.640: 20 0.640 - 0.960: 3 0.960 - 1.279: 4 1.279 - 1.599: 2 Chirality restraints: 140 Sorted by residual: chirality pdb=" CA ASN F 221 " pdb=" N ASN F 221 " pdb=" C ASN F 221 " pdb=" CB ASN F 221 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.60 2.00e-01 2.50e+01 6.39e+01 chirality pdb=" CA PHE F 222 " pdb=" N PHE F 222 " pdb=" C PHE F 222 " pdb=" CB PHE F 222 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.40e+01 chirality pdb=" CA PHE D 222 " pdb=" N PHE D 222 " pdb=" C PHE D 222 " pdb=" CB PHE D 222 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 137 not shown) Planarity restraints: 364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHI Z 216 " 0.012 2.00e-02 2.50e+03 7.47e-03 1.12e+00 pdb=" CG PHI Z 216 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHI Z 216 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHI Z 216 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHI Z 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHI Z 216 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHI Z 216 " 0.003 2.00e-02 2.50e+03 pdb=" I PHI Z 216 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY W 215 " -0.004 2.00e-02 2.50e+03 8.23e-03 6.77e-01 pdb=" C GLY W 215 " 0.014 2.00e-02 2.50e+03 pdb=" O GLY W 215 " -0.005 2.00e-02 2.50e+03 pdb=" N PHI W 216 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHI j 216 " -0.011 2.00e-02 2.50e+03 5.72e-03 6.54e-01 pdb=" CG PHI j 216 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHI j 216 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHI j 216 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHI j 216 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHI j 216 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHI j 216 " -0.003 2.00e-02 2.50e+03 pdb=" I PHI j 216 " -0.004 2.00e-02 2.50e+03 ... (remaining 361 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.51: 88 2.51 - 3.12: 1367 3.12 - 3.74: 2060 3.74 - 4.35: 2957 4.35 - 4.96: 4032 Nonbonded interactions: 10504 Sorted by model distance: nonbonded pdb=" O ASN 3 221 " pdb=" OD1 ASN 3 221 " model vdw 1.899 3.040 nonbonded pdb=" OD1 ASN j 221 " pdb=" O PHE j 222 " model vdw 1.907 3.040 nonbonded pdb=" C GLY E 223 " pdb=" OD2 ASP F 220 " model vdw 1.977 3.270 nonbonded pdb=" O ASN J 221 " pdb=" OD1 ASN J 221 " model vdw 1.991 3.040 nonbonded pdb=" O ASP p 220 " pdb=" CD2 PHE p 222 " model vdw 1.996 3.340 ... (remaining 10499 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 '0' selection = chain '3' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.130 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: 14.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.240 Find NCS groups from input model: 0.160 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 1792 Z= 0.489 Angle : 4.378 42.999 2352 Z= 2.465 Chirality : 0.340 1.599 140 Planarity : 0.002 0.008 364 Dihedral : 11.373 76.131 476 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 43.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 32.14 % 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: -5.58 (0.30), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.23), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.162 Fit side-chains REVERT: J 220 ASP cc_start: 0.7691 (p0) cc_final: 0.6646 (t0) REVERT: X 220 ASP cc_start: 0.7870 (p0) cc_final: 0.7091 (t0) REVERT: Z 220 ASP cc_start: 0.8010 (p0) cc_final: 0.7081 (m-30) REVERT: m 219 ASN cc_start: 0.7519 (p0) cc_final: 0.7179 (t0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0627 time to fit residues: 3.3148 Evaluate side-chains 15 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 ASN d 221 ASN p 219 ASN s 219 ASN ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.177 1792 Z= 2.452 Angle : 3.048 22.550 2352 Z= 1.465 Chirality : 0.151 0.460 140 Planarity : 0.015 0.046 364 Dihedral : 15.532 65.540 252 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 85.40 Ramachandran Plot: Outliers : 3.57 % Allowed : 26.43 % Favored : 70.00 % Rotamer: Outliers : 23.21 % Allowed : 23.21 % Favored : 53.57 % Cbeta Deviations : 1.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.68 % 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: -6.10 (0.34), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.26), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.079 0.010 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 7 time to evaluate : 0.164 Fit side-chains REVERT: J 222 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: W 221 ASN cc_start: 0.9045 (OUTLIER) cc_final: 0.8824 (p0) REVERT: d 221 ASN cc_start: 0.8781 (t0) cc_final: 0.8294 (t0) outliers start: 26 outliers final: 17 residues processed: 32 average time/residue: 0.0639 time to fit residues: 2.7092 Evaluate side-chains 27 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 8 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain X residue 221 ASN Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain q residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 ASN ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.8695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.181 1792 Z= 2.437 Angle : 3.097 25.826 2352 Z= 1.471 Chirality : 0.152 0.477 140 Planarity : 0.014 0.045 364 Dihedral : 16.226 61.616 252 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 104.45 Ramachandran Plot: Outliers : 8.57 % Allowed : 37.86 % Favored : 53.57 % Rotamer: Outliers : 33.04 % Allowed : 21.43 % Favored : 45.54 % Cbeta Deviations : 2.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -7.28 (0.32), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.55 (0.25), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.096 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 7 time to evaluate : 0.134 Fit side-chains REVERT: W 222 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: X 222 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7653 (p90) REVERT: c 220 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (p0) REVERT: d 221 ASN cc_start: 0.8878 (t0) cc_final: 0.8393 (t0) REVERT: s 222 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8332 (m-80) outliers start: 37 outliers final: 26 residues processed: 41 average time/residue: 0.0622 time to fit residues: 3.3867 Evaluate side-chains 37 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 7 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain m residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain q residue 221 ASN Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.8965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.183 1792 Z= 2.422 Angle : 3.110 26.049 2352 Z= 1.470 Chirality : 0.153 0.466 140 Planarity : 0.014 0.045 364 Dihedral : 16.624 61.692 252 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 110.48 Ramachandran Plot: Outliers : 6.43 % Allowed : 46.43 % Favored : 47.14 % Rotamer: Outliers : 33.93 % Allowed : 25.00 % Favored : 41.07 % Cbeta Deviations : 2.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.91 % 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: -7.59 (0.28), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.78 (0.21), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.094 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 8 time to evaluate : 0.163 Fit side-chains REVERT: J 222 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8752 (m-80) REVERT: W 222 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: X 222 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.7796 (p90) REVERT: a 220 ASP cc_start: 0.8138 (m-30) cc_final: 0.7913 (m-30) REVERT: c 220 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7972 (p0) REVERT: d 221 ASN cc_start: 0.8881 (t0) cc_final: 0.8395 (t0) REVERT: s 222 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: 3 220 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8467 (p0) outliers start: 38 outliers final: 24 residues processed: 43 average time/residue: 0.0627 time to fit residues: 3.4625 Evaluate side-chains 38 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 8 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 220 ASP Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain q residue 219 ASN Chi-restraints excluded: chain q residue 220 ASP Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 220 ASP Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.9069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.182 1792 Z= 2.413 Angle : 3.083 25.300 2352 Z= 1.457 Chirality : 0.153 0.465 140 Planarity : 0.014 0.055 364 Dihedral : 16.811 63.663 252 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 109.81 Ramachandran Plot: Outliers : 7.86 % Allowed : 48.57 % Favored : 43.57 % Rotamer: Outliers : 36.61 % Allowed : 25.00 % Favored : 38.39 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.91 % 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: -7.62 (0.27), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.80 (0.21), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.095 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 8 time to evaluate : 0.177 Fit side-chains REVERT: J 222 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: W 222 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: X 222 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8052 (p90) REVERT: d 221 ASN cc_start: 0.9018 (t0) cc_final: 0.8609 (t0) REVERT: q 222 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8112 (t80) REVERT: s 222 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: 3 220 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8484 (p0) outliers start: 41 outliers final: 23 residues processed: 46 average time/residue: 0.0615 time to fit residues: 3.6465 Evaluate side-chains 37 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 8 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 222 PHE Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 220 ASP Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.9124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.182 1792 Z= 2.409 Angle : 3.077 23.840 2352 Z= 1.453 Chirality : 0.153 0.471 140 Planarity : 0.014 0.049 364 Dihedral : 17.091 64.593 252 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 111.82 Ramachandran Plot: Outliers : 7.86 % Allowed : 49.29 % Favored : 42.86 % Rotamer: Outliers : 31.25 % Allowed : 32.14 % Favored : 36.61 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.91 % 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: -7.67 (0.27), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.096 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 8 time to evaluate : 0.127 Fit side-chains REVERT: J 222 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8739 (m-80) REVERT: W 221 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8830 (p0) REVERT: W 222 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: X 222 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8171 (p90) REVERT: d 221 ASN cc_start: 0.9067 (t0) cc_final: 0.8727 (t0) REVERT: q 222 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8204 (t80) REVERT: s 222 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: 3 220 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8484 (p0) outliers start: 35 outliers final: 23 residues processed: 40 average time/residue: 0.0559 time to fit residues: 2.9089 Evaluate side-chains 37 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 7 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 222 PHE Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 220 ASP Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.9200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.181 1792 Z= 2.409 Angle : 3.058 23.051 2352 Z= 1.451 Chirality : 0.153 0.472 140 Planarity : 0.014 0.046 364 Dihedral : 17.308 65.418 252 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 113.16 Ramachandran Plot: Outliers : 7.86 % Allowed : 50.71 % Favored : 41.43 % Rotamer: Outliers : 33.93 % Allowed : 31.25 % Favored : 34.82 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.72 (0.26), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.096 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 7 time to evaluate : 0.164 Fit side-chains REVERT: J 222 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: W 221 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8846 (p0) REVERT: W 222 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: X 222 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8187 (p90) REVERT: d 221 ASN cc_start: 0.9111 (t0) cc_final: 0.8831 (t0) REVERT: q 222 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8127 (t80) REVERT: s 222 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: 3 220 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8463 (p0) outliers start: 38 outliers final: 25 residues processed: 42 average time/residue: 0.0594 time to fit residues: 3.2453 Evaluate side-chains 39 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 7 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain W residue 219 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain e residue 221 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 222 PHE Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 220 ASP Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.9211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.181 1792 Z= 2.408 Angle : 3.056 23.051 2352 Z= 1.451 Chirality : 0.153 0.476 140 Planarity : 0.014 0.046 364 Dihedral : 17.706 80.172 252 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 113.79 Ramachandran Plot: Outliers : 7.86 % Allowed : 50.00 % Favored : 42.14 % Rotamer: Outliers : 32.14 % Allowed : 33.04 % Favored : 34.82 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.72 (0.26), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.097 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 7 time to evaluate : 0.177 Fit side-chains REVERT: J 222 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: W 221 ASN cc_start: 0.9067 (OUTLIER) cc_final: 0.8794 (p0) REVERT: W 222 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: X 222 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8243 (p90) REVERT: d 221 ASN cc_start: 0.9109 (t0) cc_final: 0.8852 (t0) REVERT: q 222 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8129 (t80) REVERT: s 222 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: 3 220 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8477 (p0) outliers start: 36 outliers final: 25 residues processed: 41 average time/residue: 0.0641 time to fit residues: 3.4207 Evaluate side-chains 39 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 7 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain e residue 221 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 222 PHE Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 220 ASP Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.9227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.181 1792 Z= 2.407 Angle : 3.055 23.063 2352 Z= 1.452 Chirality : 0.153 0.474 140 Planarity : 0.014 0.046 364 Dihedral : 17.661 75.771 252 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 113.45 Ramachandran Plot: Outliers : 7.86 % Allowed : 50.00 % Favored : 42.14 % Rotamer: Outliers : 31.25 % Allowed : 34.82 % Favored : 33.93 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.72 (0.26), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.097 0.008 PHE X 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 7 time to evaluate : 0.130 Fit side-chains REVERT: J 222 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: W 221 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (p0) REVERT: W 222 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: X 222 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8251 (p90) REVERT: d 221 ASN cc_start: 0.9109 (t0) cc_final: 0.8861 (t0) REVERT: q 222 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8134 (t80) REVERT: s 222 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7837 (m-80) REVERT: 3 220 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8456 (p0) outliers start: 35 outliers final: 26 residues processed: 40 average time/residue: 0.0626 time to fit residues: 3.2438 Evaluate side-chains 40 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 7 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain W residue 219 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain e residue 221 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 222 PHE Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 220 ASP Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.9228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.182 1792 Z= 2.406 Angle : 3.055 23.061 2352 Z= 1.453 Chirality : 0.153 0.474 140 Planarity : 0.014 0.046 364 Dihedral : 17.683 77.469 252 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 112.78 Ramachandran Plot: Outliers : 7.86 % Allowed : 50.00 % Favored : 42.14 % Rotamer: Outliers : 30.36 % Allowed : 34.82 % Favored : 34.82 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.72 (0.26), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.097 0.008 PHE X 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 7 time to evaluate : 0.163 Fit side-chains REVERT: F 222 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: J 222 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: W 221 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8792 (p0) REVERT: W 222 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7717 (m-80) REVERT: X 222 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8252 (p90) REVERT: d 221 ASN cc_start: 0.9099 (t0) cc_final: 0.8861 (t0) REVERT: q 222 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8152 (t80) REVERT: s 222 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7836 (m-80) outliers start: 34 outliers final: 26 residues processed: 40 average time/residue: 0.0627 time to fit residues: 3.2410 Evaluate side-chains 40 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 7 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain F residue 222 PHE Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 219 ASN Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain J residue 222 PHE Chi-restraints excluded: chain M residue 221 ASN Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T residue 221 ASN Chi-restraints excluded: chain W residue 219 ASN Chi-restraints excluded: chain W residue 220 ASP Chi-restraints excluded: chain W residue 221 ASN Chi-restraints excluded: chain W residue 222 PHE Chi-restraints excluded: chain X residue 222 PHE Chi-restraints excluded: chain Z residue 219 ASN Chi-restraints excluded: chain Z residue 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain e residue 221 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain m residue 221 ASN Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 222 PHE Chi-restraints excluded: chain s residue 220 ASP Chi-restraints excluded: chain s residue 222 PHE Chi-restraints excluded: chain t residue 220 ASP Chi-restraints excluded: chain w residue 221 ASN Chi-restraints excluded: chain x residue 221 ASN Chi-restraints excluded: chain 0 residue 219 ASN Chi-restraints excluded: chain 0 residue 221 ASN Chi-restraints excluded: chain 3 residue 221 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 219 ASN ** 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 = 0.4152 r_free = 0.4152 target = 0.138794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.126620 restraints weight = 1572.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.130726 restraints weight = 742.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.133597 restraints weight = 381.535| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.9238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.182 1792 Z= 2.407 Angle : 3.054 23.069 2352 Z= 1.453 Chirality : 0.154 0.474 140 Planarity : 0.014 0.046 364 Dihedral : 17.691 77.673 252 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 112.45 Ramachandran Plot: Outliers : 7.86 % Allowed : 50.00 % Favored : 42.14 % Rotamer: Outliers : 31.25 % Allowed : 33.93 % Favored : 34.82 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % 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: -7.72 (0.26), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.097 0.008 PHE X 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 399.90 seconds wall clock time: 7 minutes 44.10 seconds (464.10 seconds total)