Starting phenix.real_space_refine on Fri Apr 5 12:20:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikp_35519/04_2024/8ikp_35519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikp_35519/04_2024/8ikp_35519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikp_35519/04_2024/8ikp_35519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikp_35519/04_2024/8ikp_35519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikp_35519/04_2024/8ikp_35519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ikp_35519/04_2024/8ikp_35519_updated.pdb" } resolution = 2.98 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= 0.001 sd= 0.004 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 32 10.91 5 C 1216 2.51 5 N 352 2.21 5 O 448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 2048 Number of models: 1 Model: "" Number of chains: 32 Chain: "c" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "O" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "U" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "b" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "V" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "Y" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: "N" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 64 Classifications: {'peptide': 9} Modifications used: {'COO': 1} 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: 1.17, per 1000 atoms: 0.57 Number of scatterers: 2048 At special positions: 0 Unit cell: (117.03, 117.03, 24.9, 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 32 52.95 O 448 8.00 N 352 7.00 C 1216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 241.3 milliseconds 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 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: 0.25 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 1111 1.40 - 1.57: 937 1.57 - 1.74: 0 1.74 - 1.92: 0 1.92 - 2.09: 32 Bond restraints: 2080 Sorted by residual: bond pdb=" CZ PHI T 216 " pdb=" I PHI T 216 " ideal model delta sigma weight residual 2.106 2.012 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CZ PHI b 216 " pdb=" I PHI b 216 " ideal model delta sigma weight residual 2.106 2.013 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CZ PHI M 216 " pdb=" I PHI M 216 " ideal model delta sigma weight residual 2.106 2.014 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CZ PHI X 216 " pdb=" I PHI X 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 Z 216 " pdb=" I PHI Z 216 " ideal model delta sigma weight residual 2.106 2.014 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 2075 not shown) Histogram of bond angle deviations from ideal: 83.48 - 93.15: 6 93.15 - 102.81: 8 102.81 - 112.47: 518 112.47 - 122.14: 1753 122.14 - 131.80: 467 Bond angle restraints: 2752 Sorted by residual: angle pdb=" N GLY X 211 " pdb=" CA GLY X 211 " pdb=" C GLY X 211 " ideal model delta sigma weight residual 112.85 89.63 23.22 1.61e+00 3.86e-01 2.08e+02 angle pdb=" N PHI D 216 " pdb=" CA PHI D 216 " pdb=" CB PHI D 216 " ideal model delta sigma weight residual 110.50 131.80 -21.30 1.70e+00 3.46e-01 1.57e+02 angle pdb=" N ASN X 213 " pdb=" CA ASN X 213 " pdb=" C ASN X 213 " ideal model delta sigma weight residual 109.76 90.38 19.38 1.59e+00 3.96e-01 1.49e+02 angle pdb=" N GLY I 211 " pdb=" CA GLY I 211 " pdb=" C GLY I 211 " ideal model delta sigma weight residual 112.82 98.84 13.98 1.38e+00 5.25e-01 1.03e+02 angle pdb=" N PHI b 216 " pdb=" CA PHI b 216 " pdb=" C PHI b 216 " ideal model delta sigma weight residual 111.00 83.48 27.52 2.80e+00 1.28e-01 9.66e+01 ... (remaining 2747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 842 17.54 - 35.08: 35 35.08 - 52.62: 7 52.62 - 70.16: 5 70.16 - 87.70: 7 Dihedral angle restraints: 896 sinusoidal: 320 harmonic: 576 Sorted by residual: dihedral pdb=" N PHI D 216 " pdb=" C PHI D 216 " pdb=" CA PHI D 216 " pdb=" CB PHI D 216 " ideal model delta harmonic sigma weight residual 122.80 136.55 -13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" N PHI d 216 " pdb=" C PHI d 216 " pdb=" CA PHI d 216 " pdb=" CB PHI d 216 " ideal model delta harmonic sigma weight residual 122.80 113.06 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA GLY c 212 " pdb=" C GLY c 212 " pdb=" N ASN c 213 " pdb=" CA ASN c 213 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 140 0.063 - 0.126: 16 0.126 - 0.189: 2 0.189 - 0.252: 0 0.252 - 0.315: 2 Chirality restraints: 160 Sorted by residual: chirality pdb=" CA PHI D 216 " pdb=" N PHI D 216 " pdb=" C PHI D 216 " pdb=" CB PHI D 216 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA PHI d 216 " pdb=" N PHI d 216 " pdb=" C PHI d 216 " pdb=" CB PHI d 216 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASP X 214 " pdb=" N ASP X 214 " pdb=" C ASP X 214 " pdb=" CB ASP X 214 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 157 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY X 211 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C GLY X 211 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY X 211 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY X 212 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHI Q 216 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C PHI Q 216 " 0.022 2.00e-02 2.50e+03 pdb=" O PHI Q 216 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY Q 217 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Z 211 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C GLY Z 211 " -0.022 2.00e-02 2.50e+03 pdb=" O GLY Z 211 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY Z 212 " 0.007 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.57: 42 2.57 - 3.17: 1639 3.17 - 3.77: 2288 3.77 - 4.36: 3342 4.36 - 4.96: 4990 Nonbonded interactions: 12301 Sorted by model distance: nonbonded pdb=" O ASN X 213 " pdb=" OD1 ASP X 214 " model vdw 1.973 3.040 nonbonded pdb=" N GLY X 211 " pdb=" O GLY X 211 " model vdw 2.144 2.496 nonbonded pdb=" N PHI b 216 " pdb=" O PHI b 216 " model vdw 2.268 2.496 nonbonded pdb=" O ASN E 213 " pdb=" OD1 ASN E 213 " model vdw 2.285 3.040 nonbonded pdb=" ND2 ASN X 215 " pdb=" O PHE b 210 " model vdw 2.304 2.520 ... (remaining 12296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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=0.65 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 6.400 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 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 : 0.013 0.094 2080 Z= 0.631 Angle : 1.988 27.515 2752 Z= 0.960 Chirality : 0.054 0.315 160 Planarity : 0.003 0.033 448 Dihedral : 15.079 87.701 576 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.25 % 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: -7.03 (0.17), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.35 (0.13), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE e 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.163 Fit side-chains REVERT: Y 210 PHE cc_start: 0.6303 (m-80) cc_final: 0.3845 (p90) REVERT: K 213 ASN cc_start: 0.5368 (m-40) cc_final: 0.4866 (p0) outliers start: 0 outliers final: 1 residues processed: 40 average time/residue: 0.2709 time to fit residues: 11.6941 Evaluate side-chains 20 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 210 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 3.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN E 215 ASN F 213 ASN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 ASN R 215 ASN M 213 ASN Y 213 ASN N 213 ASN Z 215 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.266 2080 Z= 1.900 Angle : 3.204 20.578 2752 Z= 1.495 Chirality : 0.123 0.374 160 Planarity : 0.012 0.037 448 Dihedral : 20.153 87.994 322 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 10.62 % Allowed : 30.00 % Favored : 59.38 % Rotamer: Outliers : 11.72 % Allowed : 11.72 % Favored : 76.56 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.10 (0.30), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.64 (0.23), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.057 0.013 PHE f 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 6 time to evaluate : 0.145 Fit side-chains REVERT: K 213 ASN cc_start: 0.6983 (m-40) cc_final: 0.6049 (p0) outliers start: 15 outliers final: 9 residues processed: 20 average time/residue: 0.2471 time to fit residues: 5.4243 Evaluate side-chains 14 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 5 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain Z residue 210 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN P 215 ASN Y 213 ASN d 213 ASN W 215 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.7577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.273 2080 Z= 1.870 Angle : 3.260 19.200 2752 Z= 1.522 Chirality : 0.127 0.410 160 Planarity : 0.012 0.061 448 Dihedral : 20.673 87.795 322 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 1.88 % Allowed : 35.00 % Favored : 63.12 % Rotamer: Outliers : 10.94 % Allowed : 19.53 % Favored : 69.53 % Cbeta Deviations : 1.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.23), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.18), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.053 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 5 time to evaluate : 0.180 Fit side-chains REVERT: J 210 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.5965 (m-80) REVERT: K 210 PHE cc_start: 0.5808 (OUTLIER) cc_final: 0.4278 (m-80) outliers start: 14 outliers final: 8 residues processed: 17 average time/residue: 0.2668 time to fit residues: 5.0616 Evaluate side-chains 14 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 4 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP 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... Flipped N/Q/H residues before XYZ refinement: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN Y 215 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.7841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.261 2080 Z= 1.859 Angle : 3.239 20.724 2752 Z= 1.510 Chirality : 0.128 0.379 160 Planarity : 0.011 0.033 448 Dihedral : 20.392 87.222 322 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.62 % Allowed : 37.50 % Favored : 61.88 % Rotamer: Outliers : 12.50 % Allowed : 16.41 % Favored : 71.09 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.24), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.18), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.066 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 6 time to evaluate : 0.183 Fit side-chains REVERT: X 210 PHE cc_start: 0.6494 (m-80) cc_final: 0.5427 (p90) REVERT: J 210 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5903 (m-80) REVERT: K 210 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: Z 210 PHE cc_start: 0.6811 (p90) cc_final: 0.3607 (t80) outliers start: 16 outliers final: 10 residues processed: 20 average time/residue: 0.2547 time to fit residues: 5.6484 Evaluate side-chains 19 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 7 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP 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: ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.7876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.263 2080 Z= 1.858 Angle : 3.238 19.996 2752 Z= 1.508 Chirality : 0.129 0.367 160 Planarity : 0.011 0.033 448 Dihedral : 20.222 83.463 322 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 1.25 % Allowed : 36.25 % Favored : 62.50 % Rotamer: Outliers : 14.84 % Allowed : 14.84 % Favored : 70.31 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.48 (0.25), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.94 (0.19), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.068 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 6 time to evaluate : 0.138 Fit side-chains REVERT: X 210 PHE cc_start: 0.6473 (m-80) cc_final: 0.5408 (p90) REVERT: J 210 PHE cc_start: 0.7023 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: K 210 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.4463 (m-80) REVERT: Z 210 PHE cc_start: 0.6998 (p90) cc_final: 0.3734 (t80) outliers start: 19 outliers final: 10 residues processed: 23 average time/residue: 0.2740 time to fit residues: 6.9276 Evaluate side-chains 20 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 8 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: B 213 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN Y 215 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.263 2080 Z= 1.853 Angle : 3.236 19.855 2752 Z= 1.506 Chirality : 0.129 0.368 160 Planarity : 0.011 0.034 448 Dihedral : 20.223 83.239 322 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 1.25 % Allowed : 36.25 % Favored : 62.50 % Rotamer: Outliers : 14.84 % Allowed : 17.97 % Favored : 67.19 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.25), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.19), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.068 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 6 time to evaluate : 0.158 Fit side-chains REVERT: X 210 PHE cc_start: 0.6467 (m-80) cc_final: 0.5410 (p90) REVERT: J 210 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6051 (m-80) REVERT: K 210 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.4489 (m-80) REVERT: Z 210 PHE cc_start: 0.6896 (p90) cc_final: 0.3748 (t80) REVERT: f 210 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7766 (m-10) outliers start: 19 outliers final: 10 residues processed: 23 average time/residue: 0.2460 time to fit residues: 6.2189 Evaluate side-chains 20 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 7 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.7905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.264 2080 Z= 1.849 Angle : 3.234 19.819 2752 Z= 1.504 Chirality : 0.129 0.379 160 Planarity : 0.011 0.034 448 Dihedral : 20.335 83.745 322 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 1.25 % Allowed : 35.62 % Favored : 63.12 % Rotamer: Outliers : 13.28 % Allowed : 20.31 % Favored : 66.41 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.51 (0.25), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.95 (0.19), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.070 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 5 time to evaluate : 0.203 Fit side-chains REVERT: L 213 ASN cc_start: 0.7866 (OUTLIER) cc_final: 0.7536 (t0) REVERT: X 210 PHE cc_start: 0.6371 (m-80) cc_final: 0.5339 (p90) REVERT: J 210 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6037 (m-80) REVERT: K 210 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.4461 (m-80) REVERT: f 210 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7761 (m-10) outliers start: 17 outliers final: 9 residues processed: 20 average time/residue: 0.2781 time to fit residues: 6.0987 Evaluate side-chains 19 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 6 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain L residue 213 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP 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: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.263 2080 Z= 1.848 Angle : 3.232 19.807 2752 Z= 1.502 Chirality : 0.129 0.384 160 Planarity : 0.011 0.034 448 Dihedral : 20.377 84.241 322 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 1.25 % Allowed : 37.50 % Favored : 61.25 % Rotamer: Outliers : 12.50 % Allowed : 21.09 % Favored : 66.41 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.52 (0.25), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.19), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.072 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 6 time to evaluate : 0.143 Fit side-chains REVERT: X 210 PHE cc_start: 0.6391 (m-80) cc_final: 0.5344 (p90) REVERT: J 210 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6030 (m-80) REVERT: K 210 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.4460 (m-80) outliers start: 16 outliers final: 9 residues processed: 20 average time/residue: 0.2610 time to fit residues: 5.7506 Evaluate side-chains 17 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 6 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP 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: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.7946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.263 2080 Z= 1.848 Angle : 3.232 19.807 2752 Z= 1.502 Chirality : 0.129 0.388 160 Planarity : 0.011 0.034 448 Dihedral : 20.382 83.765 322 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 1.25 % Allowed : 35.62 % Favored : 63.12 % Rotamer: Outliers : 13.28 % Allowed : 21.09 % Favored : 65.62 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.48 (0.26), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.20), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.073 0.012 PHE O 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 6 time to evaluate : 0.194 Fit side-chains REVERT: X 210 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5330 (p90) REVERT: J 210 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: K 210 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.4438 (m-80) outliers start: 17 outliers final: 9 residues processed: 20 average time/residue: 0.2744 time to fit residues: 6.0670 Evaluate side-chains 20 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 8 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain X residue 210 PHE Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.7952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.265 2080 Z= 1.845 Angle : 3.232 19.918 2752 Z= 1.502 Chirality : 0.129 0.380 160 Planarity : 0.011 0.034 448 Dihedral : 20.406 83.657 322 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 1.25 % Allowed : 37.50 % Favored : 61.25 % Rotamer: Outliers : 10.94 % Allowed : 23.44 % Favored : 65.62 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.48 (0.26), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.20), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.074 0.012 PHE O 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 320 Ramachandran restraints generated. 160 Oldfield, 0 Emsley, 160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 6 time to evaluate : 0.196 Fit side-chains REVERT: X 210 PHE cc_start: 0.6391 (m-80) cc_final: 0.5349 (p90) REVERT: J 210 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: K 210 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.4457 (m-80) outliers start: 14 outliers final: 9 residues processed: 18 average time/residue: 0.2700 time to fit residues: 5.3977 Evaluate side-chains 17 residues out of total 128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 6 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain L residue 210 PHE Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain b residue 214 ASP Chi-restraints excluded: chain J residue 210 PHE Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain S residue 215 ASN Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain T residue 210 PHE Chi-restraints excluded: chain f residue 214 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 213 ASN ** f 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.262049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.253554 restraints weight = 1304.942| |-----------------------------------------------------------------------------| r_work (start): 0.4996 rms_B_bonded: 1.02 r_work: 0.4911 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.4825 rms_B_bonded: 0.84 restraints_weight: 0.2500 r_work: 0.4687 rms_B_bonded: 2.34 restraints_weight: 0.1250 r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4712 r_free = 0.4712 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4705 r_free = 0.4705 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.7964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.041 0.265 2080 Z= 1.846 Angle : 3.233 19.794 2752 Z= 1.503 Chirality : 0.129 0.372 160 Planarity : 0.011 0.035 448 Dihedral : 20.471 83.623 322 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 1.25 % Allowed : 36.25 % Favored : 62.50 % Rotamer: Outliers : 10.94 % Allowed : 24.22 % Favored : 64.84 % Cbeta Deviations : 1.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.50 (0.26), residues: 160 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.95 (0.20), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.074 0.012 PHE O 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 454.13 seconds wall clock time: 8 minutes 56.89 seconds (536.89 seconds total)