Starting phenix.real_space_refine on Mon Sep 23 11:42:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/09_2024/8ikb_35508.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/09_2024/8ikb_35508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/09_2024/8ikb_35508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/09_2024/8ikb_35508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/09_2024/8ikb_35508.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikb_35508/09_2024/8ikb_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): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 1.21, per 1000 atoms: 0.69 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: 0.43 Conformation dependent library (CDL) restraints added in 1.6 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: 0.35 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: 0.50 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: 2.980 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.690 Find NCS groups from input model: 0.100 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 1792 Z= 0.489 Angle : 4.378 42.999 2352 Z= 2.465 Chirality : 0.340 1.599 140 Planarity : 0.002 0.008 364 Dihedral : 11.373 76.131 476 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 43.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 32.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.58 (0.30), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.25 (0.23), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 280 Ramachandran restraints generated. 140 Oldfield, 0 Emsley, 140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.154 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: 0.0641 time to fit residues: 3.3600 Evaluate side-chains 15 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 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 fitting. rotamer outliers: 17 poor density : 8 time to evaluate : 0.164 Fit side-chains REVERT: J 222 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: X 222 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8299 (p90) REVERT: c 220 ASP cc_start: 0.8027 (p0) cc_final: 0.7053 (m-30) REVERT: d 221 ASN cc_start: 0.8788 (t0) cc_final: 0.8301 (t0) REVERT: q 220 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8846 (p0) outliers start: 17 outliers final: 12 residues processed: 24 average time/residue: 0.0625 time to fit residues: 2.0288 Evaluate side-chains 24 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 9 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 : 78.70 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 (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 (0.25), 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 fitting. rotamer outliers: 21 poor density : 8 time to evaluate : 0.157 Fit side-chains REVERT: P 221 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8569 (t0) REVERT: W 221 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8790 (p0) REVERT: W 222 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: X 222 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.6203 (m-10) REVERT: c 219 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: d 221 ASN cc_start: 0.8928 (t0) cc_final: 0.8507 (t0) REVERT: q 220 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.8862 (p0) REVERT: s 222 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8282 (m-80) outliers start: 21 outliers final: 12 residues processed: 28 average time/residue: 0.0610 time to fit residues: 2.2814 Evaluate side-chains 26 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 7 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.8827 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= 2.412 Angle : 3.087 23.278 2352 Z= 1.445 Chirality : 0.152 0.433 140 Planarity : 0.013 0.050 364 Dihedral : 17.514 82.134 252 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 83.36 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 0.076 0.009 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 29 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 9 time to evaluate : 0.150 Fit side-chains REVERT: J 222 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: P 221 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8503 (t0) REVERT: T 219 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8798 (t0) REVERT: W 221 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8767 (p0) REVERT: W 222 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: X 222 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.6199 (m-10) REVERT: d 221 ASN cc_start: 0.9032 (t0) cc_final: 0.8653 (t0) REVERT: s 222 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8325 (m-80) outliers start: 20 outliers final: 13 residues processed: 28 average time/residue: 0.0570 time to fit residues: 2.1508 Evaluate side-chains 28 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 8 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- 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 0.165 1792 Z= 2.404 Angle : 3.054 23.051 2352 Z= 1.430 Chirality : 0.153 0.424 140 Planarity : 0.013 0.048 364 Dihedral : 17.257 70.387 252 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 82.02 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 (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: -7.60 (0.25), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.19), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.076 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 33 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 9 time to evaluate : 0.156 Fit side-chains REVERT: J 222 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8727 (m-80) REVERT: P 221 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8486 (t0) REVERT: T 219 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8816 (t0) REVERT: W 221 ASN cc_start: 0.9039 (OUTLIER) cc_final: 0.8671 (p0) REVERT: W 222 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: c 219 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8854 (m-40) REVERT: d 221 ASN cc_start: 0.9062 (t0) cc_final: 0.8770 (t0) REVERT: q 222 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8262 (t80) REVERT: s 222 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8337 (m-80) outliers start: 24 outliers final: 14 residues processed: 32 average time/residue: 0.0638 time to fit residues: 2.7076 Evaluate side-chains 30 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 8 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.8922 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 22.934 2352 Z= 1.427 Chirality : 0.154 0.446 140 Planarity : 0.013 0.047 364 Dihedral : 17.510 78.278 252 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 83.36 Ramachandran Plot: Outliers : 2.14 % Allowed : 52.14 % 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: -7.68 (0.24), residues: 140 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.85 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.088 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 35 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 9 time to evaluate : 0.163 Fit side-chains REVERT: J 222 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: P 221 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8488 (t0) REVERT: T 219 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8823 (t0) REVERT: W 221 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8780 (p0) REVERT: W 222 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: X 222 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8385 (p90) REVERT: c 219 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8841 (m-40) REVERT: d 221 ASN cc_start: 0.9080 (t0) cc_final: 0.8852 (t0) REVERT: q 222 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8218 (t80) REVERT: s 222 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8365 (m-80) outliers start: 26 outliers final: 16 residues processed: 33 average time/residue: 0.0645 time to fit residues: 2.7852 Evaluate side-chains 34 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 9 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 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: 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: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.8944 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 22.991 2352 Z= 1.425 Chirality : 0.154 0.449 140 Planarity : 0.013 0.048 364 Dihedral : 17.495 77.286 252 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 85.37 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 36 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 9 time to evaluate : 0.164 Fit side-chains REVERT: J 222 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: P 221 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8485 (t0) REVERT: T 219 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8817 (t0) REVERT: W 221 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8629 (p0) REVERT: W 222 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: X 222 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8396 (p90) REVERT: c 219 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8854 (m-40) REVERT: q 222 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8247 (t80) REVERT: s 222 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8332 (m-80) outliers start: 27 outliers final: 16 residues processed: 33 average time/residue: 0.0575 time to fit residues: 2.5302 Evaluate side-chains 33 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 8 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.8949 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 23.309 2352 Z= 1.425 Chirality : 0.154 0.450 140 Planarity : 0.013 0.047 364 Dihedral : 17.501 77.253 252 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 85.04 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 : -5.90 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.088 0.009 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 34 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 8 time to evaluate : 0.160 Fit side-chains REVERT: J 222 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: P 221 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8486 (t0) REVERT: T 219 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8830 (t0) REVERT: W 221 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8631 (p0) REVERT: W 222 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: X 222 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8381 (p90) REVERT: c 219 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8841 (m-40) REVERT: q 222 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8249 (t80) REVERT: s 222 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8363 (m-80) outliers start: 26 outliers final: 16 residues processed: 32 average time/residue: 0.0630 time to fit residues: 2.6499 Evaluate side-chains 33 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 8 time to evaluate : 0.161 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- 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: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 22.999 2352 Z= 1.423 Chirality : 0.154 0.450 140 Planarity : 0.013 0.048 364 Dihedral : 17.537 77.195 252 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 85.70 Ramachandran Plot: Outliers : 2.86 % Allowed : 52.14 % 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 (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 (0.24), 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 *********************** 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 fitting. rotamer outliers: 26 poor density : 8 time to evaluate : 0.168 Fit side-chains REVERT: J 222 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: P 221 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8481 (t0) REVERT: W 221 ASN cc_start: 0.9036 (OUTLIER) cc_final: 0.8631 (p0) REVERT: W 222 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: X 222 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8341 (p90) REVERT: c 219 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8858 (m-40) REVERT: q 222 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8225 (t80) REVERT: s 222 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8333 (m-80) outliers start: 26 outliers final: 16 residues processed: 32 average time/residue: 0.0627 time to fit residues: 2.6534 Evaluate side-chains 32 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 8 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 0.165 1792 Z= 2.400 Angle : 3.052 23.384 2352 Z= 1.427 Chirality : 0.153 0.450 140 Planarity : 0.013 0.046 364 Dihedral : 17.476 77.102 252 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 86.04 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 (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 (0.24), 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 ********************** 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 33 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 8 time to evaluate : 0.158 Fit side-chains REVERT: J 222 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: P 221 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8481 (t0) REVERT: W 221 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8636 (p0) REVERT: W 222 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: X 222 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8340 (p90) REVERT: c 219 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8835 (m-40) REVERT: q 222 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8237 (t80) REVERT: s 222 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8365 (m-80) outliers start: 25 outliers final: 16 residues processed: 31 average time/residue: 0.0628 time to fit residues: 2.5700 Evaluate side-chains 32 residues out of total 112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 8 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 221 ASN Chi-restraints excluded: chain I residue 219 ASN Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 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: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.151343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.135676 restraints weight = 1837.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.140155 restraints weight = 824.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.142292 restraints weight = 414.903| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.8972 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 23.056 2352 Z= 1.427 Chirality : 0.154 0.450 140 Planarity : 0.013 0.047 364 Dihedral : 17.537 77.060 252 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 87.04 Ramachandran Plot: Outliers : 3.57 % Allowed : 52.14 % Favored : 44.29 % Rotamer: Outliers : 22.32 % Allowed : 30.36 % 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: -7.76 (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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 391.31 seconds wall clock time: 7 minutes 45.00 seconds (465.00 seconds total)