Starting phenix.real_space_refine on Sun Mar 17 07:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/03_2024/8izy_35877_neut_trim_updated.pdb" } resolution = 2.5 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 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: 6 Type Number sf(0) Gaussians S 36 5.16 5 C 5616 2.51 5 N 1400 2.21 5 O 1356 1.98 5 F 8 1.80 5 H 8360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ASP 262": "OD1" <-> "OD2" 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: 16776 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "B" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "C" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "D" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'9MF': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'9MF': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AVAL A 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL A 132 " occ=0.50 residue: pdb=" N AVAL B 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL B 132 " occ=0.50 residue: pdb=" N AVAL C 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL C 132 " occ=0.50 residue: pdb=" N AVAL D 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL D 132 " occ=0.50 Time building chain proxies: 14.61, per 1000 atoms: 0.87 Number of scatterers: 16776 At special positions: 0 Unit cell: (128.778, 128.778, 77.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 F 8 9.00 O 1356 8.00 N 1400 7.00 C 5616 6.00 H 8360 1.00 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: 14.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 91 through 113 Processing helix chain 'A' and resid 119 through 150 removed outlier: 4.240A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.663A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 253 Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 329 removed outlier: 3.916A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 91 through 113 Processing helix chain 'B' and resid 119 through 150 removed outlier: 4.170A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N CYS B 150 " --> pdb=" O TRP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.666A pdb=" N ALA B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 253 Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 329 removed outlier: 3.920A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'C' and resid 72 through 85 Processing helix chain 'C' and resid 91 through 113 Processing helix chain 'C' and resid 119 through 150 removed outlier: 4.238A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N CYS C 150 " --> pdb=" O TRP C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 165 removed outlier: 3.667A pdb=" N ALA C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 229 through 253 Processing helix chain 'C' and resid 264 through 275 Processing helix chain 'C' and resid 288 through 329 removed outlier: 3.922A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 91 through 113 Processing helix chain 'D' and resid 119 through 150 removed outlier: 4.237A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N CYS D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 165 removed outlier: 3.733A pdb=" N ALA D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 229 through 253 Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 329 removed outlier: 3.920A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix 616 hydrogen bonds defined for protein. 1612 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: 5.24 Time building geometry restraints manager: 14.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.23: 40 1.23 - 1.42: 3860 1.42 - 1.61: 4728 1.61 - 1.81: 48 Bond restraints: 17012 Sorted by residual: bond pdb=" C THR B 296 " pdb=" O THR B 296 " ideal model delta sigma weight residual 1.235 1.248 -0.013 1.43e-02 4.89e+03 8.27e-01 bond pdb=" CB VAL A 320 " pdb=" CG2 VAL A 320 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.98e-01 bond pdb=" C THR D 296 " pdb=" O THR D 296 " ideal model delta sigma weight residual 1.235 1.247 -0.013 1.43e-02 4.89e+03 7.71e-01 bond pdb=" CB GLU D 123 " pdb=" CG GLU D 123 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.59e-01 bond pdb=" CB VAL D 320 " pdb=" CG2 VAL D 320 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.37e-01 ... (remaining 17007 not shown) Histogram of bond angle deviations from ideal: 100.44 - 116.26: 20622 116.26 - 132.07: 9862 132.07 - 147.89: 32 147.89 - 163.70: 0 163.70 - 179.51: 8 Bond angle restraints: 30524 Sorted by residual: angle pdb=" N ARG B 213 " pdb=" CA ARG B 213 " pdb=" CB ARG B 213 " ideal model delta sigma weight residual 114.17 110.33 3.84 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" CB ARG A 213 " ideal model delta sigma weight residual 114.17 110.36 3.81 1.14e+00 7.69e-01 1.11e+01 angle pdb=" CA GLU C 123 " pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.75e+00 angle pdb=" CA GLU D 123 " pdb=" CB GLU D 123 " pdb=" CG GLU D 123 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.74e+00 angle pdb=" CA GLU A 123 " pdb=" CB GLU A 123 " pdb=" CG GLU A 123 " ideal model delta sigma weight residual 114.10 119.18 -5.08 2.00e+00 2.50e-01 6.44e+00 ... (remaining 30519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6860 17.96 - 35.91: 668 35.91 - 53.87: 250 53.87 - 71.83: 74 71.83 - 89.79: 8 Dihedral angle restraints: 7860 sinusoidal: 4080 harmonic: 3780 Sorted by residual: dihedral pdb=" CA ARG C 207 " pdb=" CB ARG C 207 " pdb=" CG ARG C 207 " pdb=" CD ARG C 207 " ideal model delta sinusoidal sigma weight residual 180.00 121.23 58.77 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG B 207 " pdb=" CB ARG B 207 " pdb=" CG ARG B 207 " pdb=" CD ARG B 207 " ideal model delta sinusoidal sigma weight residual 180.00 121.27 58.73 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG C 89 " pdb=" CB ARG C 89 " pdb=" CG ARG C 89 " pdb=" CD ARG C 89 " ideal model delta sinusoidal sigma weight residual 180.00 122.13 57.87 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 816 0.025 - 0.049: 258 0.049 - 0.074: 116 0.074 - 0.099: 52 0.099 - 0.123: 18 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CB THR A 298 " pdb=" CA THR A 298 " pdb=" OG1 THR A 298 " pdb=" CG2 THR A 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CB THR D 298 " pdb=" CA THR D 298 " pdb=" OG1 THR D 298 " pdb=" CG2 THR D 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CB THR C 298 " pdb=" CA THR C 298 " pdb=" OG1 THR C 298 " pdb=" CG2 THR C 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1257 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 214 " -0.136 9.50e-02 1.11e+02 4.55e-02 2.47e+00 pdb=" NE ARG C 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 214 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 214 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 214 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 214 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 214 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 214 " -0.135 9.50e-02 1.11e+02 4.51e-02 2.46e+00 pdb=" NE ARG D 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG D 214 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 214 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 214 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 214 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 214 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 214 " -0.135 9.50e-02 1.11e+02 4.51e-02 2.43e+00 pdb=" NE ARG B 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 214 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 214 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 214 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 214 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 214 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 214 " -0.000 2.00e-02 2.50e+03 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2342 2.26 - 2.84: 36668 2.84 - 3.43: 43940 3.43 - 4.01: 57033 4.01 - 4.60: 87766 Nonbonded interactions: 227749 Sorted by model distance: nonbonded pdb=" OE2 GLU D 254 " pdb=" H GLN D 286 " model vdw 1.671 1.850 nonbonded pdb=" OE2 GLU B 254 " pdb=" H GLN B 286 " model vdw 1.675 1.850 nonbonded pdb=" OE2 GLU A 254 " pdb=" H GLN A 286 " model vdw 1.676 1.850 nonbonded pdb=" OE2 GLU C 254 " pdb=" H GLN C 286 " model vdw 1.677 1.850 nonbonded pdb=" OD2 ASP C 212 " pdb=" HG1 THR C 217 " model vdw 1.718 1.850 ... (remaining 227744 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' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'B' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'C' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'D' and (resid 70 through 131 or resid 133 through 330 or resid 801)) } 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=0.50 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: 1.520 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: 0.250 Extract box with map and model: 4.090 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 63.070 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:10.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.003 0.029 8652 Z= 0.193 Angle : 0.533 7.678 11720 Z= 0.284 Chirality : 0.034 0.123 1260 Planarity : 0.004 0.059 1420 Dihedral : 17.628 89.785 2980 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.71 % Allowed : 28.32 % Favored : 70.97 % Cbeta Deviations : 0.00 % 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: 2.64 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.45 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 269 HIS 0.002 0.001 HIS C 324 PHE 0.009 0.001 PHE D 100 TYR 0.008 0.001 TYR D 74 ARG 0.008 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6919 (tptt) cc_final: 0.6700 (tptp) REVERT: A 214 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.7000 (mtp85) REVERT: A 324 HIS cc_start: 0.7696 (t70) cc_final: 0.7245 (t-90) REVERT: A 327 LYS cc_start: 0.7343 (tppt) cc_final: 0.6662 (tttp) REVERT: B 76 LYS cc_start: 0.6896 (tptt) cc_final: 0.6673 (tptp) REVERT: B 214 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.7004 (mtp85) REVERT: B 324 HIS cc_start: 0.7650 (t70) cc_final: 0.7201 (t-90) REVERT: B 327 LYS cc_start: 0.7339 (tppt) cc_final: 0.6657 (tttp) REVERT: C 76 LYS cc_start: 0.6930 (tptt) cc_final: 0.6709 (tptp) REVERT: C 214 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7139 (mtp85) REVERT: C 324 HIS cc_start: 0.7711 (t70) cc_final: 0.7265 (t-90) REVERT: C 327 LYS cc_start: 0.7341 (tppt) cc_final: 0.6658 (tttp) REVERT: D 162 LYS cc_start: 0.6336 (pptt) cc_final: 0.5643 (mtmm) REVERT: D 214 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.7143 (mtp85) REVERT: D 324 HIS cc_start: 0.7677 (t70) cc_final: 0.7237 (t-90) outliers start: 6 outliers final: 4 residues processed: 153 average time/residue: 2.4063 time to fit residues: 393.8721 Evaluate side-chains 136 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 132 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8652 Z= 0.282 Angle : 0.552 6.205 11720 Z= 0.304 Chirality : 0.035 0.120 1260 Planarity : 0.005 0.044 1420 Dihedral : 7.436 57.614 1168 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.03 % Allowed : 27.25 % Favored : 68.72 % Cbeta Deviations : 0.00 % 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: 2.12 (0.26), residues: 1000 helix: 1.93 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.57 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.003 0.001 HIS A 96 PHE 0.016 0.002 PHE C 304 TYR 0.012 0.001 TYR D 74 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.6631 (mtmt) cc_final: 0.6333 (pptt) REVERT: A 214 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.7162 (mtp85) REVERT: A 324 HIS cc_start: 0.7654 (t70) cc_final: 0.7212 (t-90) REVERT: B 162 LYS cc_start: 0.6636 (mtmt) cc_final: 0.6335 (pptt) REVERT: B 214 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7135 (mtp85) REVERT: B 324 HIS cc_start: 0.7646 (t70) cc_final: 0.7204 (t-90) REVERT: C 162 LYS cc_start: 0.6639 (mtmt) cc_final: 0.6343 (pptt) REVERT: C 214 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.7154 (mtp85) REVERT: C 324 HIS cc_start: 0.7651 (t70) cc_final: 0.7204 (t-90) REVERT: D 162 LYS cc_start: 0.6420 (pptt) cc_final: 0.5692 (mtmm) REVERT: D 214 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7157 (mtp85) REVERT: D 324 HIS cc_start: 0.7639 (t70) cc_final: 0.7194 (t-90) outliers start: 34 outliers final: 8 residues processed: 160 average time/residue: 2.6871 time to fit residues: 456.4774 Evaluate side-chains 143 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8652 Z= 0.207 Angle : 0.511 5.373 11720 Z= 0.278 Chirality : 0.033 0.109 1260 Planarity : 0.004 0.033 1420 Dihedral : 7.384 58.196 1168 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.79 % Allowed : 27.96 % Favored : 68.25 % Cbeta Deviations : 0.00 % 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: 1.93 (0.26), residues: 1000 helix: 1.83 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.75 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 269 HIS 0.001 0.001 HIS C 96 PHE 0.013 0.001 PHE D 297 TYR 0.013 0.001 TYR C 82 ARG 0.004 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7338 (ppt170) REVERT: A 162 LYS cc_start: 0.6591 (mtmt) cc_final: 0.6295 (pptt) REVERT: A 214 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7174 (mtp85) REVERT: A 296 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7569 (p) REVERT: A 324 HIS cc_start: 0.7645 (t70) cc_final: 0.7211 (t-90) REVERT: B 162 LYS cc_start: 0.6598 (mtmt) cc_final: 0.6298 (pptt) REVERT: B 214 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.7166 (mtp85) REVERT: B 230 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7645 (tmtt) REVERT: B 296 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7558 (p) REVERT: B 324 HIS cc_start: 0.7638 (t70) cc_final: 0.7205 (t-90) REVERT: C 87 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7344 (ppt170) REVERT: C 162 LYS cc_start: 0.6593 (mtmt) cc_final: 0.6297 (pptt) REVERT: C 214 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7155 (mtp85) REVERT: C 230 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7655 (tmtt) REVERT: C 296 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7558 (p) REVERT: C 324 HIS cc_start: 0.7645 (t70) cc_final: 0.7208 (t-90) REVERT: D 162 LYS cc_start: 0.6401 (pptt) cc_final: 0.5670 (mtmm) REVERT: D 214 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7159 (mtp85) REVERT: D 296 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7550 (p) REVERT: D 324 HIS cc_start: 0.7633 (t70) cc_final: 0.7196 (t-90) REVERT: D 325 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.5944 (ptp-170) outliers start: 32 outliers final: 14 residues processed: 155 average time/residue: 2.6838 time to fit residues: 441.1297 Evaluate side-chains 159 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 323 GLN Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8652 Z= 0.226 Angle : 0.506 4.666 11720 Z= 0.278 Chirality : 0.034 0.114 1260 Planarity : 0.004 0.029 1420 Dihedral : 7.385 57.520 1168 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.44 % Allowed : 28.08 % Favored : 68.48 % Cbeta Deviations : 0.00 % 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: 1.85 (0.26), residues: 1000 helix: 1.76 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.76 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.001 0.001 HIS C 96 PHE 0.014 0.001 PHE B 297 TYR 0.011 0.001 TYR A 82 ARG 0.003 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7360 (ppt170) REVERT: A 296 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 324 HIS cc_start: 0.7642 (t70) cc_final: 0.7213 (t-90) REVERT: B 296 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7583 (p) REVERT: B 324 HIS cc_start: 0.7635 (t70) cc_final: 0.7207 (t-90) REVERT: C 87 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7357 (ppt170) REVERT: C 296 THR cc_start: 0.8013 (OUTLIER) cc_final: 0.7582 (p) REVERT: C 324 HIS cc_start: 0.7642 (t70) cc_final: 0.7210 (t-90) REVERT: D 162 LYS cc_start: 0.6365 (pptt) cc_final: 0.5619 (mtmm) REVERT: D 296 THR cc_start: 0.8010 (OUTLIER) cc_final: 0.7575 (p) REVERT: D 324 HIS cc_start: 0.7631 (t70) cc_final: 0.7200 (t-90) outliers start: 29 outliers final: 18 residues processed: 151 average time/residue: 2.4988 time to fit residues: 401.7839 Evaluate side-chains 153 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 323 GLN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 323 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.3980 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8652 Z= 0.176 Angle : 0.493 4.496 11720 Z= 0.268 Chirality : 0.033 0.109 1260 Planarity : 0.005 0.076 1420 Dihedral : 7.399 58.462 1168 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.96 % Allowed : 29.03 % Favored : 68.01 % Cbeta Deviations : 0.00 % 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: 1.91 (0.27), residues: 1000 helix: 1.81 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.81 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 269 HIS 0.001 0.000 HIS B 324 PHE 0.012 0.001 PHE D 297 TYR 0.010 0.001 TYR C 82 ARG 0.007 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7329 (ppt170) REVERT: A 114 THR cc_start: 0.8439 (t) cc_final: 0.7898 (p) REVERT: A 162 LYS cc_start: 0.6595 (mtmt) cc_final: 0.6304 (pptt) REVERT: A 214 ARG cc_start: 0.7221 (ttm-80) cc_final: 0.6951 (mtp85) REVERT: A 296 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 324 HIS cc_start: 0.7630 (t70) cc_final: 0.7191 (t-90) REVERT: B 162 LYS cc_start: 0.6604 (mtmt) cc_final: 0.6308 (pptt) REVERT: B 214 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6945 (mtp85) REVERT: B 230 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7521 (tmtt) REVERT: B 296 THR cc_start: 0.7905 (OUTLIER) cc_final: 0.7481 (p) REVERT: B 324 HIS cc_start: 0.7623 (t70) cc_final: 0.7183 (t-90) REVERT: C 87 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7332 (ppt170) REVERT: C 114 THR cc_start: 0.8436 (t) cc_final: 0.7898 (p) REVERT: C 214 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6888 (mtp85) REVERT: C 230 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7533 (tmtt) REVERT: C 296 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7483 (p) REVERT: C 324 HIS cc_start: 0.7669 (t70) cc_final: 0.7227 (t-90) REVERT: D 114 THR cc_start: 0.8434 (t) cc_final: 0.7896 (p) REVERT: D 162 LYS cc_start: 0.6465 (pptt) cc_final: 0.5710 (mtmm) REVERT: D 214 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6862 (mtp85) REVERT: D 296 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7475 (p) REVERT: D 324 HIS cc_start: 0.7657 (t70) cc_final: 0.7214 (t-90) outliers start: 25 outliers final: 16 residues processed: 150 average time/residue: 2.4097 time to fit residues: 386.9643 Evaluate side-chains 153 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8652 Z= 0.265 Angle : 0.523 4.979 11720 Z= 0.286 Chirality : 0.035 0.117 1260 Planarity : 0.005 0.040 1420 Dihedral : 7.415 57.361 1168 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.79 % Allowed : 27.61 % Favored : 68.60 % Cbeta Deviations : 0.00 % 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: 1.80 (0.26), residues: 1000 helix: 1.72 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.72 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 269 HIS 0.002 0.001 HIS C 228 PHE 0.015 0.002 PHE D 297 TYR 0.011 0.001 TYR D 74 ARG 0.006 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7301 (ppt170) REVERT: A 114 THR cc_start: 0.8450 (t) cc_final: 0.7879 (p) REVERT: A 296 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7612 (p) REVERT: A 324 HIS cc_start: 0.7641 (t70) cc_final: 0.7204 (t-90) REVERT: B 87 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7205 (ppt170) REVERT: B 296 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7608 (p) REVERT: B 324 HIS cc_start: 0.7632 (t70) cc_final: 0.7194 (t-90) REVERT: C 87 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7295 (ppt170) REVERT: C 114 THR cc_start: 0.8446 (t) cc_final: 0.7879 (p) REVERT: C 296 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7605 (p) REVERT: C 324 HIS cc_start: 0.7638 (t70) cc_final: 0.7197 (t-90) REVERT: D 87 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7192 (ppt170) REVERT: D 114 THR cc_start: 0.8445 (t) cc_final: 0.7877 (p) REVERT: D 162 LYS cc_start: 0.6474 (pptt) cc_final: 0.5713 (mtmm) REVERT: D 296 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7599 (p) REVERT: D 324 HIS cc_start: 0.7628 (t70) cc_final: 0.7183 (t-90) REVERT: D 325 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.5837 (ptp-170) outliers start: 32 outliers final: 17 residues processed: 156 average time/residue: 2.5831 time to fit residues: 427.9783 Evaluate side-chains 155 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8652 Z= 0.207 Angle : 0.510 4.820 11720 Z= 0.277 Chirality : 0.034 0.118 1260 Planarity : 0.005 0.055 1420 Dihedral : 7.409 58.463 1168 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.67 % Allowed : 28.20 % Favored : 68.13 % Cbeta Deviations : 0.00 % 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: 1.85 (0.26), residues: 1000 helix: 1.78 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.82 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.001 0.000 HIS D 324 PHE 0.014 0.001 PHE C 297 TYR 0.010 0.001 TYR D 74 ARG 0.012 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7265 (ppt170) REVERT: A 114 THR cc_start: 0.8507 (t) cc_final: 0.7979 (p) REVERT: A 296 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7557 (p) REVERT: A 324 HIS cc_start: 0.7641 (t70) cc_final: 0.7207 (t-90) REVERT: B 83 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.6916 (t0) REVERT: B 87 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7095 (ppt170) REVERT: B 230 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7635 (tmtt) REVERT: B 296 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 324 HIS cc_start: 0.7633 (t70) cc_final: 0.7199 (t-90) REVERT: C 87 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7279 (ppt170) REVERT: C 114 THR cc_start: 0.8503 (t) cc_final: 0.7977 (p) REVERT: C 230 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7643 (tmtt) REVERT: C 296 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7554 (p) REVERT: C 324 HIS cc_start: 0.7640 (t70) cc_final: 0.7202 (t-90) REVERT: D 87 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7156 (ppt170) REVERT: D 114 THR cc_start: 0.8501 (t) cc_final: 0.7974 (p) REVERT: D 162 LYS cc_start: 0.6475 (pptt) cc_final: 0.5711 (mtmm) REVERT: D 296 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7548 (p) REVERT: D 324 HIS cc_start: 0.7617 (t70) cc_final: 0.7174 (t-90) REVERT: D 325 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5824 (ptp-170) outliers start: 31 outliers final: 16 residues processed: 154 average time/residue: 2.4209 time to fit residues: 397.9947 Evaluate side-chains 156 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8652 Z= 0.352 Angle : 0.581 6.529 11720 Z= 0.319 Chirality : 0.037 0.132 1260 Planarity : 0.006 0.066 1420 Dihedral : 7.427 58.375 1167 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.74 % Allowed : 27.01 % Favored : 68.25 % Cbeta Deviations : 0.00 % 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: 1.61 (0.26), residues: 1000 helix: 1.59 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.75 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 269 HIS 0.003 0.001 HIS B 96 PHE 0.021 0.002 PHE B 304 TYR 0.014 0.002 TYR D 74 ARG 0.015 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 131 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7326 (ppt170) REVERT: A 114 THR cc_start: 0.8478 (t) cc_final: 0.7935 (p) REVERT: A 296 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7820 (p) REVERT: A 324 HIS cc_start: 0.7650 (t70) cc_final: 0.7212 (t-90) REVERT: A 325 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.5923 (ptp-170) REVERT: B 83 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.6863 (t0) REVERT: B 87 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6969 (ppt170) REVERT: B 296 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.7817 (p) REVERT: B 324 HIS cc_start: 0.7641 (t70) cc_final: 0.7202 (t-90) REVERT: B 325 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5925 (ptp-170) REVERT: C 87 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7280 (ppt170) REVERT: C 114 THR cc_start: 0.8474 (t) cc_final: 0.7936 (p) REVERT: C 296 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7817 (p) REVERT: C 324 HIS cc_start: 0.7646 (t70) cc_final: 0.7203 (t-90) REVERT: C 325 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.5918 (ptp-170) REVERT: D 87 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7143 (ppt170) REVERT: D 114 THR cc_start: 0.8470 (t) cc_final: 0.7931 (p) REVERT: D 162 LYS cc_start: 0.6479 (pptt) cc_final: 0.5730 (mtmm) REVERT: D 296 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7811 (p) REVERT: D 324 HIS cc_start: 0.7633 (t70) cc_final: 0.7189 (t-90) REVERT: D 325 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5831 (ptp-170) outliers start: 40 outliers final: 21 residues processed: 158 average time/residue: 2.3891 time to fit residues: 403.1069 Evaluate side-chains 162 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 323 GLN Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8652 Z= 0.209 Angle : 0.523 4.926 11720 Z= 0.285 Chirality : 0.034 0.124 1260 Planarity : 0.006 0.071 1420 Dihedral : 7.399 58.150 1167 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.03 % Allowed : 27.73 % Favored : 68.25 % Cbeta Deviations : 0.00 % 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: 1.74 (0.26), residues: 1000 helix: 1.71 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.94 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.001 0.000 HIS C 324 PHE 0.013 0.001 PHE C 297 TYR 0.010 0.001 TYR D 74 ARG 0.012 0.001 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7304 (ppt170) REVERT: A 114 THR cc_start: 0.8489 (t) cc_final: 0.7986 (p) REVERT: A 296 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7642 (p) REVERT: A 324 HIS cc_start: 0.7686 (t70) cc_final: 0.7255 (t-90) REVERT: A 325 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.5825 (ptp-170) REVERT: B 83 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.6840 (t0) REVERT: B 87 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6943 (ppt170) REVERT: B 296 THR cc_start: 0.8083 (OUTLIER) cc_final: 0.7640 (p) REVERT: B 324 HIS cc_start: 0.7678 (t70) cc_final: 0.7247 (t-90) REVERT: B 325 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.5830 (ptp-170) REVERT: C 87 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7317 (ppt170) REVERT: C 114 THR cc_start: 0.8484 (t) cc_final: 0.7984 (p) REVERT: C 296 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7639 (p) REVERT: C 324 HIS cc_start: 0.7682 (t70) cc_final: 0.7246 (t-90) REVERT: C 325 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5824 (ptp-170) REVERT: D 87 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7125 (ppt170) REVERT: D 114 THR cc_start: 0.8482 (t) cc_final: 0.7982 (p) REVERT: D 162 LYS cc_start: 0.6353 (pptt) cc_final: 0.5579 (mtmm) REVERT: D 296 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7634 (p) REVERT: D 324 HIS cc_start: 0.7621 (t70) cc_final: 0.7183 (t-90) REVERT: D 325 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.5832 (ptp-170) outliers start: 34 outliers final: 18 residues processed: 158 average time/residue: 2.4587 time to fit residues: 417.7404 Evaluate side-chains 160 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8652 Z= 0.181 Angle : 0.511 5.351 11720 Z= 0.279 Chirality : 0.034 0.113 1260 Planarity : 0.006 0.075 1420 Dihedral : 7.419 57.910 1167 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.44 % Allowed : 28.44 % Favored : 68.13 % Cbeta Deviations : 0.00 % 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: 1.89 (0.26), residues: 1000 helix: 1.79 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.79 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.001 0.000 HIS D 324 PHE 0.014 0.001 PHE B 297 TYR 0.009 0.001 TYR D 74 ARG 0.012 0.001 ARG C 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 129 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7331 (ppt170) REVERT: A 114 THR cc_start: 0.8497 (t) cc_final: 0.8007 (p) REVERT: A 296 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7563 (p) REVERT: A 324 HIS cc_start: 0.7669 (t70) cc_final: 0.7227 (t-90) REVERT: A 325 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5851 (ptp-170) REVERT: B 83 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.6896 (t0) REVERT: B 87 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7041 (ppt170) REVERT: B 296 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7562 (p) REVERT: B 324 HIS cc_start: 0.7661 (t70) cc_final: 0.7220 (t-90) REVERT: B 325 ARG cc_start: 0.6707 (OUTLIER) cc_final: 0.5853 (ptp-170) REVERT: C 87 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7324 (ppt170) REVERT: C 114 THR cc_start: 0.8488 (t) cc_final: 0.8002 (p) REVERT: C 296 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 324 HIS cc_start: 0.7675 (t70) cc_final: 0.7244 (t-90) REVERT: C 325 ARG cc_start: 0.6711 (OUTLIER) cc_final: 0.5848 (ptp-170) REVERT: D 83 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.6826 (t0) REVERT: D 87 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7001 (ppt170) REVERT: D 114 THR cc_start: 0.8486 (t) cc_final: 0.8000 (p) REVERT: D 162 LYS cc_start: 0.6491 (pptt) cc_final: 0.5724 (mtmm) REVERT: D 296 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7553 (p) REVERT: D 324 HIS cc_start: 0.7653 (t70) cc_final: 0.7220 (t-90) REVERT: D 325 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.5795 (ptp-170) outliers start: 29 outliers final: 14 residues processed: 151 average time/residue: 2.4532 time to fit residues: 395.2642 Evaluate side-chains 150 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 325 ARG Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.174806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123735 restraints weight = 77670.194| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.02 r_work: 0.3383 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8652 Z= 0.179 Angle : 0.508 5.214 11720 Z= 0.277 Chirality : 0.034 0.112 1260 Planarity : 0.005 0.072 1420 Dihedral : 7.227 58.073 1164 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.44 % Allowed : 28.91 % Favored : 67.65 % Cbeta Deviations : 0.00 % 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: 1.87 (0.26), residues: 1000 helix: 1.79 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.84 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.001 0.000 HIS C 324 PHE 0.014 0.001 PHE B 297 TYR 0.009 0.001 TYR D 74 ARG 0.012 0.001 ARG A 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7037.09 seconds wall clock time: 122 minutes 55.64 seconds (7375.64 seconds total)