Starting phenix.real_space_refine on Mon Mar 11 11:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddy_27382/03_2024/8ddy_27382_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddy_27382/03_2024/8ddy_27382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddy_27382/03_2024/8ddy_27382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddy_27382/03_2024/8ddy_27382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddy_27382/03_2024/8ddy_27382_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ddy_27382/03_2024/8ddy_27382_updated.pdb" } resolution = 2.89 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 129 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 3 4.86 5 C 4860 2.51 5 N 1284 2.21 5 O 1773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ARG 125": "NH1" <-> "NH2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ASP 130": "OD1" <-> "OD2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ASP 130": "OD1" <-> "OD2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "F TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7968 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1226 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "B" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1233 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1226 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "D" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1233 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1226 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain: "F" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1233 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'CYC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'CYC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {' CL': 1, 'CYC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "F" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Time building chain proxies: 5.04, per 1000 atoms: 0.63 Number of scatterers: 7968 At special positions: 0 Unit cell: (123.968, 127.296, 80.704, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 3 17.00 S 48 16.00 O 1773 8.00 N 1284 7.00 C 4860 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.515A pdb=" N ARG A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 136 through 143 Processing helix chain 'A' and resid 147 through 164 Processing helix chain 'A' and resid 169 through 183 Proline residue: A 175 - end of helix Processing helix chain 'B' and resid 4 through 15 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 35 through 46 Processing helix chain 'B' and resid 48 through 59 Processing helix chain 'B' and resid 75 through 97 Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.840A pdb=" N ILE B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 60 through 72 Processing helix chain 'C' and resid 74 through 88 removed outlier: 3.515A pdb=" N ARG C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 136 through 143 Processing helix chain 'C' and resid 147 through 164 Processing helix chain 'C' and resid 169 through 183 Proline residue: C 175 - end of helix Processing helix chain 'D' and resid 4 through 15 Proline residue: D 11 - end of helix Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 48 through 59 Processing helix chain 'D' and resid 75 through 97 Processing helix chain 'D' and resid 103 through 106 No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.840A pdb=" N ILE D 156 " --> pdb=" O TYR D 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 47 through 57 Processing helix chain 'E' and resid 60 through 72 Processing helix chain 'E' and resid 74 through 88 removed outlier: 3.514A pdb=" N ARG E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 122 Processing helix chain 'E' and resid 126 through 131 Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 147 through 164 Processing helix chain 'E' and resid 169 through 183 Proline residue: E 175 - end of helix Processing helix chain 'F' and resid 4 through 15 Proline residue: F 11 - end of helix Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 35 through 46 Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 75 through 97 Processing helix chain 'F' and resid 103 through 106 No H-bonds generated for 'chain 'F' and resid 103 through 106' Processing helix chain 'F' and resid 112 through 119 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 143 through 159 removed outlier: 3.839A pdb=" N ILE F 156 " --> pdb=" O TYR F 152 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1422 hydrogen bond angles 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: 2.22 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1281 1.29 - 1.42: 1827 1.42 - 1.55: 4548 1.55 - 1.68: 27 1.68 - 1.81: 81 Bond restraints: 7764 Sorted by residual: bond pdb=" NB CYC F 201 " pdb=" C4B CYC F 201 " ideal model delta sigma weight residual 1.369 1.524 -0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" NB CYC B 201 " pdb=" C4B CYC B 201 " ideal model delta sigma weight residual 1.369 1.524 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" NB CYC D 201 " pdb=" C4B CYC D 201 " ideal model delta sigma weight residual 1.369 1.524 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" NB CYC B 201 " pdb=" C1B CYC B 201 " ideal model delta sigma weight residual 1.377 1.528 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NB CYC D 201 " pdb=" C1B CYC D 201 " ideal model delta sigma weight residual 1.377 1.528 -0.151 2.00e-02 2.50e+03 5.66e+01 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 95.72 - 104.60: 138 104.60 - 113.48: 4202 113.48 - 122.36: 5131 122.36 - 131.25: 1002 131.25 - 140.13: 45 Bond angle restraints: 10518 Sorted by residual: angle pdb=" CA ARG A 151 " pdb=" CB ARG A 151 " pdb=" CG ARG A 151 " ideal model delta sigma weight residual 114.10 134.13 -20.03 2.00e+00 2.50e-01 1.00e+02 angle pdb=" CA ARG E 151 " pdb=" CB ARG E 151 " pdb=" CG ARG E 151 " ideal model delta sigma weight residual 114.10 134.09 -19.99 2.00e+00 2.50e-01 9.99e+01 angle pdb=" CA ARG C 151 " pdb=" CB ARG C 151 " pdb=" CG ARG C 151 " ideal model delta sigma weight residual 114.10 134.06 -19.96 2.00e+00 2.50e-01 9.96e+01 angle pdb=" CB ARG E 151 " pdb=" CG ARG E 151 " pdb=" CD ARG E 151 " ideal model delta sigma weight residual 111.30 131.69 -20.39 2.30e+00 1.89e-01 7.86e+01 angle pdb=" CB ARG C 151 " pdb=" CG ARG C 151 " pdb=" CD ARG C 151 " ideal model delta sigma weight residual 111.30 131.67 -20.37 2.30e+00 1.89e-01 7.84e+01 ... (remaining 10513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4303 17.05 - 34.10: 428 34.10 - 51.15: 81 51.15 - 68.19: 60 68.19 - 85.24: 21 Dihedral angle restraints: 4893 sinusoidal: 2097 harmonic: 2796 Sorted by residual: dihedral pdb=" CA GLN B 32 " pdb=" C GLN B 32 " pdb=" N SER B 33 " pdb=" CA SER B 33 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN F 32 " pdb=" C GLN F 32 " pdb=" N SER F 33 " pdb=" CA SER F 33 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN D 32 " pdb=" C GLN D 32 " pdb=" N SER D 33 " pdb=" CA SER D 33 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 4890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 782 0.059 - 0.117: 305 0.117 - 0.176: 68 0.176 - 0.234: 13 0.234 - 0.293: 8 Chirality restraints: 1176 Sorted by residual: chirality pdb=" CG LEU E 45 " pdb=" CB LEU E 45 " pdb=" CD1 LEU E 45 " pdb=" CD2 LEU E 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CG LEU A 45 " pdb=" CB LEU A 45 " pdb=" CD1 LEU A 45 " pdb=" CD2 LEU A 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU C 45 " pdb=" CB LEU C 45 " pdb=" CD1 LEU C 45 " pdb=" CD2 LEU C 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1173 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 62 " -0.017 2.00e-02 2.50e+03 2.97e-02 1.77e+01 pdb=" CG TYR B 62 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 62 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 62 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 62 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 62 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 62 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 62 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 62 " 0.017 2.00e-02 2.50e+03 2.97e-02 1.76e+01 pdb=" CG TYR F 62 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR F 62 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR F 62 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR F 62 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 62 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 62 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 62 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 62 " -0.017 2.00e-02 2.50e+03 2.96e-02 1.76e+01 pdb=" CG TYR D 62 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR D 62 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR D 62 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR D 62 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 62 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 62 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 62 " 0.004 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1548 2.78 - 3.31: 7762 3.31 - 3.84: 14787 3.84 - 4.37: 18526 4.37 - 4.90: 28700 Nonbonded interactions: 71323 Sorted by model distance: nonbonded pdb=" OE1 GLN B 128 " pdb=" O HOH B 301 " model vdw 2.247 2.440 nonbonded pdb=" OE1 GLN D 128 " pdb=" O HOH D 301 " model vdw 2.252 2.440 nonbonded pdb=" OE1 GLN F 128 " pdb=" O HOH F 301 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR E 118 " pdb=" O SER F 17 " model vdw 2.264 2.440 nonbonded pdb=" NH2 ARG E 151 " pdb=" O ILE E 181 " model vdw 2.277 2.520 ... (remaining 71318 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' 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=1.00 max=1.00 mean=1.00 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.220 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.770 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:14.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.016 0.155 7764 Z= 1.019 Angle : 1.753 20.388 10518 Z= 0.863 Chirality : 0.067 0.293 1176 Planarity : 0.009 0.071 1335 Dihedral : 16.382 85.243 3087 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.82 % Allowed : 4.58 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.48 (0.24), residues: 933 helix: -1.18 (0.16), residues: 804 sheet: None (None), residues: 0 loop : -3.44 (0.43), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 86 HIS 0.002 0.001 HIS D 155 PHE 0.025 0.004 PHE E 85 TYR 0.071 0.005 TYR B 62 ARG 0.030 0.004 ARG E 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 55 ASP cc_start: 0.6874 (m-30) cc_final: 0.6554 (t70) REVERT: A 79 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6150 (pp30) REVERT: B 14 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: B 54 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8271 (mtmm) REVERT: C 151 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5969 (mmm160) REVERT: D 107 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7202 (mmm160) REVERT: F 3 ASP cc_start: 0.8458 (p0) cc_final: 0.8208 (p0) REVERT: F 107 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7034 (mmp80) REVERT: F 128 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7164 (tm-30) outliers start: 30 outliers final: 2 residues processed: 184 average time/residue: 1.9206 time to fit residues: 366.4376 Evaluate side-chains 133 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain C residue 151 ARG Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain F residue 107 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN B 131 ASN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7764 Z= 0.167 Angle : 0.644 10.530 10518 Z= 0.303 Chirality : 0.037 0.123 1176 Planarity : 0.005 0.046 1335 Dihedral : 10.419 81.776 1340 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.91 % Allowed : 11.96 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.27 (0.27), residues: 933 helix: 0.37 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -3.30 (0.44), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 86 HIS 0.000 0.000 HIS D 155 PHE 0.014 0.001 PHE E 85 TYR 0.015 0.002 TYR D 152 ARG 0.007 0.000 ARG E 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 79 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6333 (pt0) REVERT: B 14 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: B 54 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8166 (mtmt) REVERT: B 133 MET cc_start: 0.8581 (ttm) cc_final: 0.8254 (ttm) REVERT: C 168 GLU cc_start: 0.5895 (OUTLIER) cc_final: 0.5541 (tp30) REVERT: D 107 ARG cc_start: 0.7550 (mmt90) cc_final: 0.7090 (mmt-90) REVERT: E 54 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6771 (mm-30) REVERT: E 154 MET cc_start: 0.8064 (mmt) cc_final: 0.7741 (mmt) REVERT: F 107 ARG cc_start: 0.7482 (mmt90) cc_final: 0.7180 (mpt180) outliers start: 15 outliers final: 4 residues processed: 150 average time/residue: 1.7336 time to fit residues: 270.9633 Evaluate side-chains 140 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 134 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 117 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7764 Z= 0.156 Angle : 0.601 10.578 10518 Z= 0.277 Chirality : 0.037 0.124 1176 Planarity : 0.004 0.053 1335 Dihedral : 9.367 77.691 1317 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.53 % Allowed : 15.65 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.85 (0.27), residues: 933 helix: 1.14 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -3.07 (0.46), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.011 0.001 PHE E 85 TYR 0.013 0.002 TYR D 87 ARG 0.006 0.000 ARG E 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 0.882 Fit side-chains REVERT: B 14 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6984 (pt0) REVERT: B 54 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8164 (mtmm) REVERT: B 133 MET cc_start: 0.8594 (ttm) cc_final: 0.8331 (ttm) REVERT: C 168 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5655 (tp30) REVERT: D 107 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7074 (mmt-90) REVERT: E 28 MET cc_start: 0.7359 (ttm) cc_final: 0.6870 (ttm) REVERT: E 54 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6718 (mm-30) REVERT: E 84 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7329 (mtt180) REVERT: F 107 ARG cc_start: 0.7491 (mmt90) cc_final: 0.7174 (mpt180) REVERT: F 128 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6787 (tt0) outliers start: 12 outliers final: 3 residues processed: 156 average time/residue: 1.5589 time to fit residues: 254.1774 Evaluate side-chains 145 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 GLN C 33 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7764 Z= 0.151 Angle : 0.585 10.474 10518 Z= 0.269 Chirality : 0.036 0.123 1176 Planarity : 0.004 0.044 1335 Dihedral : 9.082 75.711 1317 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.67 % Allowed : 16.28 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.42 (0.28), residues: 933 helix: 1.54 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -2.90 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 111 HIS 0.000 0.000 HIS D 155 PHE 0.011 0.001 PHE C 85 TYR 0.013 0.001 TYR D 152 ARG 0.004 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6316 (ptt180) REVERT: A 74 GLU cc_start: 0.7678 (tt0) cc_final: 0.7447 (tt0) REVERT: A 80 GLU cc_start: 0.7706 (tp30) cc_final: 0.7296 (tp30) REVERT: B 14 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6881 (mm-30) REVERT: B 29 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6512 (ptt-90) REVERT: B 54 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8224 (mtmt) REVERT: B 83 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8410 (ptt90) REVERT: B 133 MET cc_start: 0.8596 (ttm) cc_final: 0.8332 (ttm) REVERT: B 154 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: C 43 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6107 (ptt180) REVERT: C 154 MET cc_start: 0.8060 (mmp) cc_final: 0.7721 (mmp) REVERT: C 168 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5757 (tp30) REVERT: D 107 ARG cc_start: 0.7495 (mmt90) cc_final: 0.7082 (mmt-90) REVERT: E 28 MET cc_start: 0.7349 (ttm) cc_final: 0.6828 (ttm) REVERT: E 54 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6795 (mm-30) REVERT: E 84 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7275 (mtt180) REVERT: F 107 ARG cc_start: 0.7498 (mmt90) cc_final: 0.7165 (mpt180) REVERT: F 128 GLN cc_start: 0.7102 (tm-30) cc_final: 0.6769 (tt0) outliers start: 21 outliers final: 3 residues processed: 161 average time/residue: 1.7170 time to fit residues: 287.9745 Evaluate side-chains 154 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 84 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN B 32 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7764 Z= 0.228 Angle : 0.648 10.580 10518 Z= 0.299 Chirality : 0.039 0.122 1176 Planarity : 0.004 0.038 1335 Dihedral : 9.002 77.925 1317 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.29 % Allowed : 18.70 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.45 (0.28), residues: 933 helix: 1.55 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.93 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 111 HIS 0.001 0.001 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.014 0.002 TYR D 91 ARG 0.004 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.904 Fit side-chains REVERT: A 43 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.6428 (ptt180) REVERT: A 80 GLU cc_start: 0.7709 (tp30) cc_final: 0.7344 (tp30) REVERT: B 14 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: B 29 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6625 (ptt-90) REVERT: B 54 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8355 (mtmm) REVERT: B 106 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6657 (pp20) REVERT: B 133 MET cc_start: 0.8573 (ttm) cc_final: 0.8337 (ttm) REVERT: C 43 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.6209 (ptt180) REVERT: C 168 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5716 (tp30) REVERT: D 154 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: E 54 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6806 (mm-30) REVERT: F 107 ARG cc_start: 0.7571 (mmt90) cc_final: 0.7345 (mpt180) REVERT: F 128 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6746 (tt0) REVERT: F 154 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7015 (m-30) outliers start: 18 outliers final: 3 residues processed: 157 average time/residue: 1.6804 time to fit residues: 275.1181 Evaluate side-chains 154 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7764 Z= 0.204 Angle : 0.631 10.549 10518 Z= 0.291 Chirality : 0.038 0.136 1176 Planarity : 0.004 0.037 1335 Dihedral : 8.848 76.535 1317 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.42 % Allowed : 19.08 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.56 (0.28), residues: 933 helix: 1.63 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.89 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.001 0.001 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.019 0.002 TYR D 152 ARG 0.006 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.886 Fit side-chains REVERT: A 43 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.6472 (ptt180) REVERT: A 80 GLU cc_start: 0.7616 (tp30) cc_final: 0.7196 (tp30) REVERT: B 54 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8309 (mtmt) REVERT: B 107 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7473 (ttm170) REVERT: B 133 MET cc_start: 0.8573 (ttm) cc_final: 0.8353 (ttm) REVERT: C 43 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.6207 (ptt180) REVERT: C 168 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5777 (tp30) REVERT: D 14 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: D 42 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7760 (ttpt) REVERT: D 107 ARG cc_start: 0.7616 (mmt-90) cc_final: 0.6783 (mmt180) REVERT: E 43 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.6917 (ptt90) REVERT: E 54 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6759 (mm-30) REVERT: E 76 LYS cc_start: 0.8302 (tttm) cc_final: 0.7961 (ttpt) REVERT: F 107 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7306 (mpt180) REVERT: F 128 GLN cc_start: 0.7071 (tm-30) cc_final: 0.6770 (tt0) REVERT: F 154 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7016 (m-30) outliers start: 19 outliers final: 5 residues processed: 155 average time/residue: 1.7007 time to fit residues: 274.8966 Evaluate side-chains 154 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 29 ARG Chi-restraints excluded: chain F residue 36 MET Chi-restraints excluded: chain F residue 154 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7764 Z= 0.164 Angle : 0.600 10.493 10518 Z= 0.276 Chirality : 0.037 0.123 1176 Planarity : 0.004 0.036 1335 Dihedral : 8.330 69.042 1314 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.29 % Allowed : 19.97 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.77 (0.28), residues: 933 helix: 1.75 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.75 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.016 0.001 TYR D 87 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6466 (ptt180) REVERT: A 80 GLU cc_start: 0.7652 (tp30) cc_final: 0.7394 (tp30) REVERT: B 54 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8356 (mtmm) REVERT: B 106 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: C 43 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.6145 (ptt180) REVERT: C 168 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5742 (tp30) REVERT: D 14 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: D 107 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.6792 (mmt180) REVERT: E 43 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.6721 (ptt90) REVERT: E 54 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6757 (mm-30) REVERT: E 74 GLU cc_start: 0.7759 (tt0) cc_final: 0.7493 (tt0) REVERT: E 76 LYS cc_start: 0.8298 (tttm) cc_final: 0.7949 (ttpt) REVERT: F 107 ARG cc_start: 0.7449 (mmt90) cc_final: 0.7235 (mpt180) REVERT: F 128 GLN cc_start: 0.7050 (tm-30) cc_final: 0.6721 (tt0) outliers start: 18 outliers final: 5 residues processed: 155 average time/residue: 1.6589 time to fit residues: 268.1163 Evaluate side-chains 157 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 29 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 106 GLN B 32 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7764 Z= 0.183 Angle : 0.618 10.533 10518 Z= 0.285 Chirality : 0.037 0.122 1176 Planarity : 0.004 0.037 1335 Dihedral : 8.255 68.472 1314 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.54 % Allowed : 19.85 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.78 (0.28), residues: 933 helix: 1.75 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.72 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.019 0.002 TYR D 152 ARG 0.009 0.000 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.6514 (ptt180) REVERT: A 50 ILE cc_start: 0.8153 (mm) cc_final: 0.7948 (mp) REVERT: A 80 GLU cc_start: 0.7609 (tp30) cc_final: 0.7257 (tp30) REVERT: B 54 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8297 (mtmt) REVERT: B 106 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6726 (pp20) REVERT: C 43 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.6179 (ptt180) REVERT: C 168 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5734 (tp30) REVERT: D 14 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: D 107 ARG cc_start: 0.7571 (mmt-90) cc_final: 0.6770 (mmt180) REVERT: D 154 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6827 (m-30) REVERT: E 43 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.6875 (ptt90) REVERT: E 54 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6750 (mm-30) REVERT: E 74 GLU cc_start: 0.7785 (tt0) cc_final: 0.7453 (tt0) REVERT: E 76 LYS cc_start: 0.8363 (tttm) cc_final: 0.7995 (ttpt) REVERT: F 107 ARG cc_start: 0.7485 (mmt90) cc_final: 0.7261 (mpt180) REVERT: F 128 GLN cc_start: 0.7039 (tm-30) cc_final: 0.6726 (tt0) outliers start: 20 outliers final: 8 residues processed: 158 average time/residue: 1.6679 time to fit residues: 274.8630 Evaluate side-chains 161 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7764 Z= 0.194 Angle : 0.626 10.531 10518 Z= 0.289 Chirality : 0.038 0.122 1176 Planarity : 0.004 0.038 1335 Dihedral : 8.203 67.931 1314 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.42 % Allowed : 19.85 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.75 (0.28), residues: 933 helix: 1.76 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.87 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.019 0.002 TYR B 87 ARG 0.010 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 0.962 Fit side-chains REVERT: A 43 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.6532 (ptt180) REVERT: A 80 GLU cc_start: 0.7596 (tp30) cc_final: 0.7191 (tp30) REVERT: B 54 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8294 (mtmt) REVERT: B 106 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6754 (pp20) REVERT: C 43 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6182 (ptt180) REVERT: C 168 GLU cc_start: 0.6079 (OUTLIER) cc_final: 0.5746 (tp30) REVERT: D 14 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: D 107 ARG cc_start: 0.7616 (mmt-90) cc_final: 0.6814 (mmt180) REVERT: D 154 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: E 43 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.6870 (ptt90) REVERT: E 54 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6752 (mm-30) REVERT: E 76 LYS cc_start: 0.8359 (tttm) cc_final: 0.7983 (ttpt) REVERT: F 107 ARG cc_start: 0.7497 (mmt90) cc_final: 0.7274 (mpt180) REVERT: F 128 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6736 (tt0) outliers start: 19 outliers final: 7 residues processed: 155 average time/residue: 1.7332 time to fit residues: 281.4721 Evaluate side-chains 159 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 29 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 75 GLN E 98 ASN F 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7764 Z= 0.205 Angle : 0.637 10.544 10518 Z= 0.295 Chirality : 0.038 0.122 1176 Planarity : 0.004 0.038 1335 Dihedral : 8.199 67.948 1314 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.16 % Allowed : 20.36 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.71 (0.28), residues: 933 helix: 1.70 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -2.70 (0.50), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.012 0.001 PHE C 85 TYR 0.023 0.002 TYR D 152 ARG 0.009 0.001 ARG B 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1866 Ramachandran restraints generated. 933 Oldfield, 0 Emsley, 933 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.949 Fit side-chains REVERT: A 43 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.6551 (ptt180) REVERT: A 50 ILE cc_start: 0.8157 (mm) cc_final: 0.7945 (mp) REVERT: A 80 GLU cc_start: 0.7595 (tp30) cc_final: 0.7281 (tp30) REVERT: B 14 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6631 (tp30) REVERT: B 54 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8297 (mtmt) REVERT: C 43 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.6194 (ptt180) REVERT: C 168 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5781 (tp30) REVERT: D 14 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: D 107 ARG cc_start: 0.7639 (mmt-90) cc_final: 0.6873 (mmt180) REVERT: D 154 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6889 (m-30) REVERT: E 43 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.6854 (ptt90) REVERT: E 54 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6756 (mm-30) REVERT: E 76 LYS cc_start: 0.8358 (tttm) cc_final: 0.7977 (ttpt) REVERT: F 107 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7278 (mpt180) REVERT: F 128 GLN cc_start: 0.7034 (tm-30) cc_final: 0.6735 (tt0) outliers start: 17 outliers final: 7 residues processed: 153 average time/residue: 1.7503 time to fit residues: 279.3069 Evaluate side-chains 153 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 84 ARG Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 98 ASN F 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.111275 restraints weight = 9274.524| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.07 r_work: 0.3040 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7764 Z= 0.186 Angle : 0.625 10.531 10518 Z= 0.290 Chirality : 0.038 0.123 1176 Planarity : 0.004 0.041 1335 Dihedral : 8.139 68.257 1314 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.78 % Allowed : 20.87 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.79 (0.28), residues: 933 helix: 1.78 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.82 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 111 HIS 0.001 0.000 HIS D 155 PHE 0.013 0.001 PHE C 85 TYR 0.022 0.002 TYR D 87 ARG 0.009 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4367.10 seconds wall clock time: 77 minutes 42.62 seconds (4662.62 seconds total)