Starting phenix.real_space_refine on Tue Feb 3 12:20:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikb_35508/02_2026/8ikb_35508.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikb_35508/02_2026/8ikb_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_35508/02_2026/8ikb_35508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikb_35508/02_2026/8ikb_35508.map" model { file = "/net/cci-nas-00/data/ceres_data/8ikb_35508/02_2026/8ikb_35508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikb_35508/02_2026/8ikb_35508.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 0.51, per 1000 atoms: 0.29 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: 0.17 Conformation dependent library (CDL) restraints added in 46.0 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: 0.39 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: 0.22 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: 7.410 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: 0.010 Set scattering table: 0.010 Process input model: 4.230 Find NCS groups from input model: 0.040 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 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 : 43.19 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.00918 ( 1792) covalent geometry : angle 4.37810 ( 2352) *********************** 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 : 0.055 Fit side-chains REVERT: J 220 ASP cc_start: 0.7685 (p0) cc_final: 0.6643 (t0) REVERT: X 220 ASP cc_start: 0.7865 (p0) cc_final: 0.7094 (t0) REVERT: Z 220 ASP cc_start: 0.8008 (p0) cc_final: 0.7082 (m-30) REVERT: m 219 ASN cc_start: 0.7517 (p0) cc_final: 0.7179 (t0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0252 time to fit residues: 1.3649 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 : 0.054 ------------------------------------------------------------------------------- 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 = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.136553 restraints weight = 2019.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.141038 restraints weight = 949.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144551 restraints weight = 459.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.145440 restraints weight = 248.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.145436 restraints weight = 167.681| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 70.30 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.05004 ( 1792) covalent geometry : angle 3.03243 ( 2352) *********************** 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 : 0.035 Fit side-chains REVERT: J 222 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: X 222 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8224 (p90) REVERT: c 220 ASP cc_start: 0.7969 (p0) cc_final: 0.7006 (m-30) REVERT: d 221 ASN cc_start: 0.8655 (t0) cc_final: 0.8217 (t0) REVERT: q 220 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8600 (p0) outliers start: 17 outliers final: 12 residues processed: 24 average time/residue: 0.0150 time to fit residues: 0.5329 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 : 0.034 ------------------------------------------------------------------------------- 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: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.136065 restraints weight = 1891.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.141120 restraints weight = 865.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144198 restraints weight = 413.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.145271 restraints weight = 212.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.145266 restraints weight = 165.792| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.8543 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= 2.425 Angle : 3.081 25.293 2352 Z= 1.447 Chirality : 0.152 0.433 140 Planarity : 0.013 0.044 364 Dihedral : 16.447 62.647 252 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 78.65 Ramachandran Plot: Outliers : 2.86 % Allowed : 42.14 % Favored : 55.00 % Rotamer: Outliers : 18.75 % Allowed : 21.43 % Favored : 59.82 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.08 (0.32), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.39 (0.25), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.075 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04974 ( 1792) covalent geometry : angle 3.08142 ( 2352) *********************** 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 : 0.058 Fit side-chains REVERT: P 221 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8518 (t0) REVERT: W 221 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8584 (p0) REVERT: W 222 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: X 222 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.6301 (m-10) REVERT: c 219 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8519 (m-40) REVERT: d 221 ASN cc_start: 0.8755 (t0) cc_final: 0.8397 (t0) REVERT: q 220 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8614 (p0) REVERT: s 222 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8111 (m-80) outliers start: 21 outliers final: 12 residues processed: 28 average time/residue: 0.0235 time to fit residues: 0.9110 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 : 0.054 ------------------------------------------------------------------------------- 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: 0.8980 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 = 0.4195 r_free = 0.4195 target = 0.151187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.135311 restraints weight = 1868.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.140675 restraints weight = 868.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.142959 restraints weight = 417.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.145180 restraints weight = 248.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.145173 restraints weight = 151.009| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.8828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 0.166 1792 Z= 2.413 Angle : 3.087 23.303 2352 Z= 1.445 Chirality : 0.153 0.433 140 Planarity : 0.013 0.050 364 Dihedral : 17.518 82.209 252 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 83.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 0.076 0.008 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04956 ( 1792) covalent geometry : angle 3.08684 ( 2352) *********************** 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 29 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 9 time to evaluate : 0.061 Fit side-chains REVERT: J 222 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: P 221 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8438 (t0) REVERT: T 219 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8794 (t0) REVERT: W 221 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8585 (p0) REVERT: W 222 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: X 222 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.6302 (m-10) REVERT: d 221 ASN cc_start: 0.8859 (t0) cc_final: 0.8533 (t0) REVERT: s 222 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8146 (m-80) outliers start: 20 outliers final: 13 residues processed: 28 average time/residue: 0.0267 time to fit residues: 1.0250 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 : 0.060 ------------------------------------------------------------------------------- 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 X residue 222 PHE 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 219 ASN M 219 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.152207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.135164 restraints weight = 1868.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.139901 restraints weight = 945.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143318 restraints weight = 460.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144009 restraints weight = 233.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.145564 restraints weight = 174.550| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.8892 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= 2.405 Angle : 3.054 23.050 2352 Z= 1.430 Chirality : 0.153 0.423 140 Planarity : 0.013 0.048 364 Dihedral : 17.271 71.317 252 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 82.33 Ramachandran Plot: Outliers : 2.86 % Allowed : 48.57 % Favored : 48.57 % Rotamer: Outliers : 21.43 % Allowed : 29.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.60 (0.25), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.78 (0.19), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.076 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04936 ( 1792) covalent geometry : angle 3.05379 ( 2352) *********************** 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 33 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 9 time to evaluate : 0.034 Fit side-chains REVERT: J 222 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: P 221 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8438 (t0) REVERT: T 219 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8831 (t0) REVERT: W 221 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8484 (p0) REVERT: W 222 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: c 219 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8621 (m-40) REVERT: d 221 ASN cc_start: 0.8894 (t0) cc_final: 0.8639 (t0) REVERT: q 222 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8146 (t80) REVERT: s 222 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8148 (m-80) outliers start: 24 outliers final: 14 residues processed: 32 average time/residue: 0.0151 time to fit residues: 0.6594 Evaluate side-chains 30 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 8 time to evaluate : 0.033 ------------------------------------------------------------------------------- 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 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 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: 0.8980 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 = 0.4182 r_free = 0.4182 target = 0.141085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.127873 restraints weight = 1470.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.131591 restraints weight = 704.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.134452 restraints weight = 375.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.136313 restraints weight = 204.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.136712 restraints weight = 119.699| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 0.167 1792 Z= 2.405 Angle : 3.049 22.916 2352 Z= 1.428 Chirality : 0.154 0.445 140 Planarity : 0.013 0.047 364 Dihedral : 17.500 78.004 252 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 83.67 Ramachandran Plot: Outliers : 2.14 % Allowed : 50.71 % Favored : 47.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.67 (0.24), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.19), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.088 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04936 ( 1792) covalent geometry : angle 3.04941 ( 2352) *********************** 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 35 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 9 time to evaluate : 0.055 Fit side-chains REVERT: J 222 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: P 221 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8444 (t0) REVERT: T 219 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8834 (t0) REVERT: W 221 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8635 (p0) REVERT: W 222 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: X 222 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8339 (p90) REVERT: c 219 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8667 (m-40) REVERT: d 221 ASN cc_start: 0.8937 (t0) cc_final: 0.8737 (t0) REVERT: q 222 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8131 (t80) REVERT: s 222 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8225 (m-80) outliers start: 26 outliers final: 16 residues processed: 33 average time/residue: 0.0234 time to fit residues: 1.0418 Evaluate side-chains 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 9 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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 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: 1.9990 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 = 0.4169 r_free = 0.4169 target = 0.140188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.127752 restraints weight = 1475.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.131831 restraints weight = 699.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.134880 restraints weight = 353.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.134930 restraints weight = 182.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.135166 restraints weight = 163.777| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.8942 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= 2.404 Angle : 3.048 23.050 2352 Z= 1.426 Chirality : 0.154 0.449 140 Planarity : 0.013 0.047 364 Dihedral : 17.487 77.274 252 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 85.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Details of bonding type rmsd covalent geometry : bond 0.04932 ( 1792) covalent geometry : angle 3.04800 ( 2352) *********************** 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 36 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 9 time to evaluate : 0.057 Fit side-chains REVERT: J 222 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8661 (m-80) REVERT: P 221 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8436 (t0) REVERT: T 219 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8833 (t0) REVERT: W 221 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8492 (p0) REVERT: W 222 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: X 222 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8345 (p90) REVERT: c 219 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8688 (m-40) REVERT: q 222 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8210 (t80) REVERT: s 222 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8220 (m-80) outliers start: 27 outliers final: 16 residues processed: 33 average time/residue: 0.0234 time to fit residues: 1.0514 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 : 0.055 ------------------------------------------------------------------------------- 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 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 = 0.4197 r_free = 0.4197 target = 0.151040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.134927 restraints weight = 1844.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.138919 restraints weight = 900.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.142316 restraints weight = 479.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.143502 restraints weight = 252.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.143343 restraints weight = 199.038| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.8950 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 : 3.048 23.108 2352 Z= 1.425 Chirality : 0.154 0.450 140 Planarity : 0.013 0.047 364 Dihedral : 17.512 77.258 252 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 84.67 Ramachandran Plot: Outliers : 2.86 % Allowed : 52.14 % Favored : 45.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.74 (0.24), 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 0.088 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04928 ( 1792) covalent geometry : angle 3.04754 ( 2352) *********************** 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 33 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 8 time to evaluate : 0.058 Fit side-chains REVERT: J 222 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: P 221 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8420 (t0) REVERT: T 219 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8839 (t0) REVERT: W 221 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8461 (p0) REVERT: W 222 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7441 (m-80) REVERT: X 222 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8260 (p90) REVERT: c 219 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8631 (m-40) REVERT: q 222 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8194 (t80) REVERT: s 222 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.8207 (m-80) outliers start: 25 outliers final: 15 residues processed: 32 average time/residue: 0.0220 time to fit residues: 0.9648 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 : 0.033 ------------------------------------------------------------------------------- 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=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 = 0.4175 r_free = 0.4175 target = 0.140575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.127417 restraints weight = 1515.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.131582 restraints weight = 724.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.134229 restraints weight = 362.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134193 restraints weight = 187.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.134193 restraints weight = 187.158| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.8962 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 : 3.045 23.012 2352 Z= 1.424 Chirality : 0.154 0.449 140 Planarity : 0.013 0.048 364 Dihedral : 17.537 77.192 252 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 85.01 Ramachandran Plot: Outliers : 3.57 % Allowed : 51.43 % Favored : 45.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -7.75 (0.24), 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 0.088 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04925 ( 1792) covalent geometry : angle 3.04533 ( 2352) *********************** 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 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 8 time to evaluate : 0.034 Fit side-chains REVERT: J 222 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8653 (m-80) REVERT: P 221 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8435 (t0) REVERT: T 219 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8849 (t0) REVERT: W 221 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8499 (p0) REVERT: W 222 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: X 222 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8287 (p90) REVERT: c 219 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8683 (m-40) REVERT: q 222 PHE cc_start: 0.8978 (OUTLIER) cc_final: 0.8180 (t80) REVERT: s 222 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8227 (m-80) outliers start: 26 outliers final: 16 residues processed: 32 average time/residue: 0.0230 time to fit residues: 0.9857 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 : 0.037 ------------------------------------------------------------------------------- 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 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 = 0.4205 r_free = 0.4205 target = 0.151480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.134948 restraints weight = 1781.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.139630 restraints weight = 882.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.141386 restraints weight = 430.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.143809 restraints weight = 285.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144271 restraints weight = 158.266| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.8964 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 : 3.052 23.379 2352 Z= 1.427 Chirality : 0.154 0.450 140 Planarity : 0.013 0.047 364 Dihedral : 17.490 77.100 252 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 86.01 Ramachandran Plot: Outliers : 2.86 % Allowed : 51.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 0.088 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04923 ( 1792) covalent geometry : angle 3.05153 ( 2352) ********************** 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 34 residues out of total 112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 8 time to evaluate : 0.050 Fit side-chains REVERT: J 222 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: P 221 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8421 (t0) REVERT: W 221 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8451 (p0) REVERT: W 222 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: X 222 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.8266 (p90) REVERT: c 219 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8611 (m-40) REVERT: q 222 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8090 (t80) REVERT: s 222 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8164 (m-80) outliers start: 26 outliers final: 16 residues processed: 32 average time/residue: 0.0194 time to fit residues: 0.8522 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 : 0.035 ------------------------------------------------------------------------------- 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 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 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 = 0.4173 r_free = 0.4173 target = 0.140384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.127387 restraints weight = 1538.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.131800 restraints weight = 724.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.134473 restraints weight = 354.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.135098 restraints weight = 183.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.135098 restraints weight = 151.300| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.8971 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 : 3.049 23.052 2352 Z= 1.428 Chirality : 0.153 0.449 140 Planarity : 0.013 0.049 364 Dihedral : 17.536 77.063 252 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 87.35 Ramachandran Plot: Outliers : 3.57 % Allowed : 52.14 % Favored : 44.29 % Rotamer: Outliers : 21.43 % Allowed : 31.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 0.088 0.009 PHE X 222 Details of bonding type rmsd covalent geometry : bond 0.04918 ( 1792) covalent geometry : angle 3.04949 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 318.05 seconds wall clock time: 6 minutes 8.71 seconds (368.71 seconds total)