Starting phenix.real_space_refine on Wed Mar 5 14:33:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikb_35508/03_2025/8ikb_35508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikb_35508/03_2025/8ikb_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/cci-nas-00/data/ceres_data/8ikb_35508/03_2025/8ikb_35508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikb_35508/03_2025/8ikb_35508.map" model { file = "/net/cci-nas-00/data/ceres_data/8ikb_35508/03_2025/8ikb_35508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikb_35508/03_2025/8ikb_35508.cif" } 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. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 1.24, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 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: 0.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.58 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: 0.55 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: 0.00 - 8.60: 2203 8.60 - 17.20: 104 17.20 - 25.80: 39 25.80 - 34.40: 5 34.40 - 43.00: 1 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 Time spend for trying shortcut: 0.00 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: 0.000 Normalize map: mean=0, sd=1: 3.830 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.820 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.147 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: 0.0577 time to fit residues: 3.0593 Evaluate side-chains 15 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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: a 221 ASN c 221 ASN d 221 ASN p 219 ASN x 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.153737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.135530 restraints weight = 2009.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.141094 restraints weight = 915.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.144361 restraints weight = 448.341| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.7924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.174 1792 Z= 2.447 Angle : 3.032 22.396 2352 Z= 1.449 Chirality : 0.156 0.473 140 Planarity : 0.015 0.044 364 Dihedral : 16.082 63.637 252 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 70.35 Ramachandran Plot: Outliers : 3.57 % Allowed : 22.86 % Favored : 73.57 % Rotamer: Outliers : 15.18 % Allowed : 18.75 % Favored : 66.07 % Cbeta Deviations : 1.43 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -5.84 (0.34), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.45 (0.26), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.073 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 25 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 8 time to evaluate : 0.158 Fit side-chains REVERT: J 222 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: X 222 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8213 (p90) REVERT: c 220 ASP cc_start: 0.7968 (p0) cc_final: 0.7006 (m-30) REVERT: d 221 ASN cc_start: 0.8653 (t0) cc_final: 0.8217 (t0) REVERT: q 220 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8594 (p0) outliers start: 17 outliers final: 12 residues processed: 24 average time/residue: 0.0782 time to fit residues: 2.4632 Evaluate side-chains 24 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 9 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I 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 X residue 222 PHE 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 221 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.152786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.136085 restraints weight = 1860.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.141186 restraints weight = 927.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143981 restraints weight = 428.163| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.8525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.170 1792 Z= 2.426 Angle : 3.076 25.297 2352 Z= 1.444 Chirality : 0.152 0.435 140 Planarity : 0.013 0.043 364 Dihedral : 16.433 62.380 252 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 78.37 Ramachandran Plot: Outliers : 2.14 % Allowed : 42.86 % Favored : 55.00 % Rotamer: Outliers : 18.75 % Allowed : 22.32 % Favored : 58.93 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.12 % 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: -7.08 (0.32), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.24), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.075 0.009 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 29 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 8 time to evaluate : 0.169 Fit side-chains REVERT: P 221 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8458 (t0) REVERT: W 221 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8598 (p0) REVERT: W 222 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: X 222 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8384 (p90) REVERT: c 219 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8514 (m-40) REVERT: d 221 ASN cc_start: 0.8791 (t0) cc_final: 0.8421 (t0) REVERT: q 220 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8759 (p0) REVERT: s 222 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8176 (m-80) outliers start: 21 outliers final: 12 residues processed: 28 average time/residue: 0.0806 time to fit residues: 2.8941 Evaluate side-chains 26 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 7 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 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 c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP 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 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.151530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.135466 restraints weight = 1847.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.140248 restraints weight = 890.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.141398 restraints weight = 426.793| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.167 1792 Z= 2.413 Angle : 3.097 23.195 2352 Z= 1.448 Chirality : 0.152 0.431 140 Planarity : 0.013 0.041 364 Dihedral : 17.257 68.547 252 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 83.70 Ramachandran Plot: Outliers : 3.57 % Allowed : 47.14 % Favored : 49.29 % Rotamer: Outliers : 17.86 % Allowed : 28.57 % Favored : 53.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.46 % 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: -7.55 (0.26), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.75 (0.20), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.077 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 28 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 8 time to evaluate : 0.159 Fit side-chains REVERT: J 222 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: P 221 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8425 (t0) REVERT: T 219 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8762 (t0) REVERT: W 221 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8567 (p0) REVERT: W 222 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7417 (m-80) REVERT: c 219 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8652 (m-40) REVERT: d 221 ASN cc_start: 0.8831 (t0) cc_final: 0.8514 (t0) REVERT: s 222 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: 0 220 ASP cc_start: 0.8755 (p0) cc_final: 0.8545 (p0) outliers start: 20 outliers final: 13 residues processed: 27 average time/residue: 0.0597 time to fit residues: 2.1846 Evaluate side-chains 28 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 8 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 220 ASP 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 c residue 219 ASN Chi-restraints excluded: chain m 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 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: F 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.151610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.135871 restraints weight = 1857.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.140278 restraints weight = 883.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.143289 restraints weight = 431.914| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.8893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.166 1792 Z= 2.406 Angle : 3.051 23.046 2352 Z= 1.428 Chirality : 0.154 0.453 140 Planarity : 0.013 0.050 364 Dihedral : 17.279 69.316 252 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 81.69 Ramachandran Plot: Outliers : 2.86 % Allowed : 50.00 % Favored : 47.14 % Rotamer: Outliers : 24.11 % Allowed : 25.89 % Favored : 50.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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 (0.25), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.80 (0.19), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.087 0.009 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 36 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 9 time to evaluate : 0.175 Fit side-chains REVERT: J 222 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: P 221 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8419 (t0) REVERT: T 219 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8838 (t0) REVERT: W 221 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8514 (p0) REVERT: W 222 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: X 222 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7947 (p90) REVERT: c 219 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8679 (m-40) REVERT: d 221 ASN cc_start: 0.8900 (t0) cc_final: 0.8649 (t0) REVERT: q 222 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8179 (t80) REVERT: s 222 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: 0 220 ASP cc_start: 0.8784 (p0) cc_final: 0.8579 (p0) outliers start: 27 outliers final: 15 residues processed: 34 average time/residue: 0.0881 time to fit residues: 3.8461 Evaluate side-chains 32 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 8 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP 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 221 ASN 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.141508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.128276 restraints weight = 1439.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.131261 restraints weight = 671.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.134045 restraints weight = 378.638| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.8923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.166 1792 Z= 2.406 Angle : 3.049 23.098 2352 Z= 1.426 Chirality : 0.154 0.454 140 Planarity : 0.013 0.049 364 Dihedral : 17.545 78.674 252 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 85.04 Ramachandran Plot: Outliers : 2.86 % Allowed : 50.71 % Favored : 46.43 % Rotamer: Outliers : 22.32 % Allowed : 28.57 % Favored : 49.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -7.69 (0.24), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.86 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.009 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 33 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 8 time to evaluate : 0.179 Fit side-chains REVERT: J 222 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8639 (m-80) REVERT: P 221 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8437 (t0) REVERT: T 219 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8844 (t0) REVERT: W 221 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8530 (p0) REVERT: W 222 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: X 222 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8029 (p90) REVERT: c 219 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8706 (m-40) REVERT: q 222 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8214 (t80) REVERT: s 222 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: 0 220 ASP cc_start: 0.8819 (p0) cc_final: 0.8612 (p0) outliers start: 25 outliers final: 16 residues processed: 31 average time/residue: 0.0679 time to fit residues: 2.7949 Evaluate side-chains 32 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 7 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain q residue 219 ASN 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 221 ASN 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: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.139912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.127455 restraints weight = 1511.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.131552 restraints weight = 707.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.132266 restraints weight = 358.590| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.8948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.166 1792 Z= 2.403 Angle : 3.047 23.077 2352 Z= 1.425 Chirality : 0.154 0.452 140 Planarity : 0.013 0.048 364 Dihedral : 17.528 77.237 252 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 85.04 Ramachandran Plot: Outliers : 2.86 % Allowed : 51.43 % Favored : 45.71 % Rotamer: Outliers : 24.11 % Allowed : 28.57 % Favored : 47.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -7.73 (0.24), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.009 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 35 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 8 time to evaluate : 0.210 Fit side-chains REVERT: J 222 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: P 221 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8432 (t0) REVERT: T 219 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8836 (t0) REVERT: W 221 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8507 (p0) REVERT: W 222 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: X 222 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8013 (p90) REVERT: c 219 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8734 (m-40) REVERT: q 222 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8260 (t80) REVERT: s 222 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: 0 220 ASP cc_start: 0.8815 (p0) cc_final: 0.8606 (p0) outliers start: 27 outliers final: 17 residues processed: 32 average time/residue: 0.0912 time to fit residues: 3.7364 Evaluate side-chains 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 8 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 219 ASN 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 221 ASN 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: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.151442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.135444 restraints weight = 1866.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.138974 restraints weight = 822.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.142842 restraints weight = 465.676| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.8952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.165 1792 Z= 2.403 Angle : 3.046 23.251 2352 Z= 1.424 Chirality : 0.154 0.452 140 Planarity : 0.013 0.047 364 Dihedral : 17.533 77.322 252 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 84.70 Ramachandran Plot: Outliers : 2.86 % Allowed : 52.14 % Favored : 45.00 % Rotamer: Outliers : 23.21 % Allowed : 28.57 % Favored : 48.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -7.74 (0.24), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.89 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 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 35 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 9 time to evaluate : 0.180 Fit side-chains REVERT: J 222 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: P 221 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8424 (t0) REVERT: T 219 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8839 (t0) REVERT: W 221 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8471 (p0) REVERT: W 222 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: X 222 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8006 (p90) REVERT: c 219 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (m-40) REVERT: q 222 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8197 (t80) REVERT: s 222 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: 0 220 ASP cc_start: 0.8787 (p0) cc_final: 0.8571 (p0) outliers start: 26 outliers final: 17 residues processed: 33 average time/residue: 0.0687 time to fit residues: 3.0257 Evaluate side-chains 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 8 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 219 ASN 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 221 ASN 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: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127330 restraints weight = 1527.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.131180 restraints weight = 720.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.133418 restraints weight = 354.822| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.049 0.166 1792 Z= 2.402 Angle : 3.042 23.010 2352 Z= 1.421 Chirality : 0.154 0.452 140 Planarity : 0.013 0.049 364 Dihedral : 17.571 77.286 252 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 85.37 Ramachandran Plot: Outliers : 2.86 % Allowed : 52.14 % Favored : 45.00 % Rotamer: Outliers : 25.00 % Allowed : 27.68 % Favored : 47.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -7.75 (0.23), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.90 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 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 36 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 8 time to evaluate : 0.195 Fit side-chains REVERT: J 222 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: P 221 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8434 (t0) REVERT: T 219 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8837 (t0) REVERT: W 221 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8497 (p0) REVERT: W 222 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: X 222 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8022 (p90) REVERT: c 219 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8706 (m-40) REVERT: q 222 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8217 (t80) REVERT: s 222 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: 0 220 ASP cc_start: 0.8825 (p0) cc_final: 0.8610 (p0) outliers start: 28 outliers final: 17 residues processed: 34 average time/residue: 0.0733 time to fit residues: 3.3003 Evaluate side-chains 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 8 time to evaluate : 0.164 ------------------------------------------------------------------------------- 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 219 ASN 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 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: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.134921 restraints weight = 1947.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.139857 restraints weight = 861.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.143139 restraints weight = 419.609| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.8969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.166 1792 Z= 2.401 Angle : 3.049 23.352 2352 Z= 1.426 Chirality : 0.153 0.452 140 Planarity : 0.013 0.047 364 Dihedral : 17.539 77.206 252 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 85.70 Ramachandran Plot: Outliers : 3.57 % Allowed : 50.71 % Favored : 45.71 % Rotamer: Outliers : 23.21 % Allowed : 27.68 % Favored : 49.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -7.76 (0.23), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.009 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 35 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 9 time to evaluate : 0.229 Fit side-chains REVERT: J 222 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: P 221 ASN cc_start: 0.8851 (OUTLIER) cc_final: 0.8418 (t0) REVERT: T 219 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8839 (t0) REVERT: W 221 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8455 (p0) REVERT: W 222 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: X 222 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8003 (p90) REVERT: c 219 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8638 (m-40) REVERT: q 222 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8172 (t80) REVERT: s 222 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8179 (m-80) REVERT: 0 220 ASP cc_start: 0.8791 (p0) cc_final: 0.8579 (p0) outliers start: 26 outliers final: 17 residues processed: 33 average time/residue: 0.0951 time to fit residues: 4.1008 Evaluate side-chains 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 8 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 222 PHE Chi-restraints excluded: chain P residue 221 ASN Chi-restraints excluded: chain S residue 221 ASN Chi-restraints excluded: chain T 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 220 ASP Chi-restraints excluded: chain a residue 219 ASN Chi-restraints excluded: chain c residue 219 ASN Chi-restraints excluded: chain m residue 220 ASP Chi-restraints excluded: chain p residue 222 PHE Chi-restraints excluded: chain q residue 219 ASN 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 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: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.140306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.127754 restraints weight = 1541.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.131422 restraints weight = 730.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.133051 restraints weight = 366.145| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.8973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.049 0.166 1792 Z= 2.400 Angle : 3.046 23.052 2352 Z= 1.424 Chirality : 0.153 0.452 140 Planarity : 0.013 0.046 364 Dihedral : 17.589 77.179 252 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 87.04 Ramachandran Plot: Outliers : 3.57 % Allowed : 52.14 % Favored : 44.29 % Rotamer: Outliers : 23.21 % Allowed : 29.46 % Favored : 47.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.02 % 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: -7.77 (0.23), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.92 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.009 PHE X 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 539.22 seconds wall clock time: 10 minutes 18.63 seconds (618.63 seconds total)