Starting phenix.real_space_refine on Wed Feb 14 18:39:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv9_7637/02_2024/6cv9_7637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv9_7637/02_2024/6cv9_7637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv9_7637/02_2024/6cv9_7637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv9_7637/02_2024/6cv9_7637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv9_7637/02_2024/6cv9_7637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cv9_7637/02_2024/6cv9_7637.pdb" } resolution = 3.8 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6272 2.51 5 N 1740 2.21 5 O 1964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2508 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2508 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2508 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2508 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 5.60, per 1000 atoms: 0.56 Number of scatterers: 10032 At special positions: 0 Unit cell: (114.21, 114.21, 107.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1964 8.00 N 1740 7.00 C 6272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 70.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.826A pdb=" N ALA A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 226 through 237 removed outlier: 3.750A pdb=" N GLU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.649A pdb=" N SER A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 272 " --> pdb=" O HIS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 337 removed outlier: 3.604A pdb=" N LEU A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 874 Processing helix chain 'A' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.827A pdb=" N ALA B 163 " --> pdb=" O ARG B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 226 through 237 removed outlier: 3.751A pdb=" N GLU B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.648A pdb=" N SER B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 removed outlier: 3.605A pdb=" N LEU B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 874 Processing helix chain 'B' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU B 883 " --> pdb=" O ASN B 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 108 Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.827A pdb=" N ALA C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 226 through 237 removed outlier: 3.751A pdb=" N GLU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 removed outlier: 3.648A pdb=" N SER C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Proline residue: C 292 - end of helix Processing helix chain 'C' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 337 removed outlier: 3.605A pdb=" N LEU C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 874 Processing helix chain 'C' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU C 883 " --> pdb=" O ASN C 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 144 through 154 removed outlier: 3.601A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.827A pdb=" N ALA D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 219 through 225 Processing helix chain 'D' and resid 226 through 237 removed outlier: 3.751A pdb=" N GLU D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.648A pdb=" N SER D 258 " --> pdb=" O CYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 removed outlier: 3.685A pdb=" N SER D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 272 " --> pdb=" O HIS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 278 removed outlier: 3.995A pdb=" N LYS D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 300 removed outlier: 3.504A pdb=" N LEU D 287 " --> pdb=" O ALA D 283 " (cutoff:3.500A) Proline residue: D 292 - end of helix Processing helix chain 'D' and resid 305 through 325 removed outlier: 3.592A pdb=" N LYS D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 337 removed outlier: 3.605A pdb=" N LEU D 332 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 874 Processing helix chain 'D' and resid 879 through 921 removed outlier: 4.143A pdb=" N LEU D 883 " --> pdb=" O ASN D 879 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1752 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: 2.40 Time building geometry restraints manager: 4.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2997 1.33 - 1.45: 1391 1.45 - 1.57: 5708 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10176 Sorted by residual: bond pdb=" N LEU B 238 " pdb=" CA LEU B 238 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.28e-02 6.10e+03 4.15e+00 bond pdb=" N LEU D 238 " pdb=" CA LEU D 238 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.28e-02 6.10e+03 4.15e+00 bond pdb=" N LEU C 238 " pdb=" CA LEU C 238 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.28e-02 6.10e+03 4.15e+00 bond pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta sigma weight residual 1.456 1.431 0.026 1.28e-02 6.10e+03 4.01e+00 bond pdb=" CB PHE C 266 " pdb=" CG PHE C 266 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.65e+00 ... (remaining 10171 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.32: 207 106.32 - 112.88: 5400 112.88 - 119.43: 3103 119.43 - 125.99: 4906 125.99 - 132.55: 88 Bond angle restraints: 13704 Sorted by residual: angle pdb=" N LEU B 238 " pdb=" CA LEU B 238 " pdb=" C LEU B 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.53e+01 angle pdb=" N LEU C 238 " pdb=" CA LEU C 238 " pdb=" C LEU C 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.53e+01 angle pdb=" N LEU D 238 " pdb=" CA LEU D 238 " pdb=" C LEU D 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.53e+01 angle pdb=" N LEU A 238 " pdb=" CA LEU A 238 " pdb=" C LEU A 238 " ideal model delta sigma weight residual 110.10 102.61 7.49 1.49e+00 4.50e-01 2.52e+01 angle pdb=" C ASN A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta sigma weight residual 120.33 124.29 -3.96 8.00e-01 1.56e+00 2.45e+01 ... (remaining 13699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 5991 14.33 - 28.66: 273 28.66 - 42.99: 60 42.99 - 57.32: 4 57.32 - 71.65: 4 Dihedral angle restraints: 6332 sinusoidal: 2584 harmonic: 3748 Sorted by residual: dihedral pdb=" CA ASP A 204 " pdb=" C ASP A 204 " pdb=" N PHE A 205 " pdb=" CA PHE A 205 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP D 204 " pdb=" C ASP D 204 " pdb=" N PHE D 205 " pdb=" CA PHE D 205 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ASP B 204 " pdb=" C ASP B 204 " pdb=" N PHE B 205 " pdb=" CA PHE B 205 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 6329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 914 0.042 - 0.083: 453 0.083 - 0.124: 137 0.124 - 0.165: 20 0.165 - 0.206: 16 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE C 273 " pdb=" N ILE C 273 " pdb=" C ILE C 273 " pdb=" CB ILE C 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE D 273 " pdb=" N ILE D 273 " pdb=" C ILE D 273 " pdb=" CB ILE D 273 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1537 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 143 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLU D 143 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU D 143 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS D 144 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 143 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLU C 143 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU C 143 " 0.014 2.00e-02 2.50e+03 pdb=" N HIS C 144 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 143 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C GLU B 143 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU B 143 " -0.014 2.00e-02 2.50e+03 pdb=" N HIS B 144 " -0.012 2.00e-02 2.50e+03 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3095 2.83 - 3.35: 9834 3.35 - 3.87: 15792 3.87 - 4.38: 17920 4.38 - 4.90: 29817 Nonbonded interactions: 76458 Sorted by model distance: nonbonded pdb=" OE1 GLU A 885 " pdb=" NZ LYS B 887 " model vdw 2.316 2.520 nonbonded pdb=" O GLU A 899 " pdb=" OG SER A 902 " model vdw 2.333 2.440 nonbonded pdb=" O GLU D 899 " pdb=" OG SER D 902 " model vdw 2.333 2.440 nonbonded pdb=" O GLU C 899 " pdb=" OG SER C 902 " model vdw 2.333 2.440 nonbonded pdb=" O GLU B 899 " pdb=" OG SER B 902 " model vdw 2.333 2.440 ... (remaining 76453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.320 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 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 : 0.006 0.079 10176 Z= 0.406 Angle : 0.998 8.098 13704 Z= 0.572 Chirality : 0.053 0.206 1540 Planarity : 0.006 0.034 1792 Dihedral : 9.512 71.650 3892 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -3.93 (0.18), residues: 1248 helix: -1.85 (0.14), residues: 848 sheet: None (None), residues: 0 loop : -4.11 (0.23), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 227 PHE 0.030 0.003 PHE D 313 TYR 0.035 0.003 TYR A 317 ARG 0.006 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 1.252 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: A 99 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8019 (pt0) REVERT: A 266 PHE cc_start: 0.8359 (t80) cc_final: 0.8101 (t80) REVERT: A 267 SER cc_start: 0.8503 (t) cc_final: 0.8246 (p) REVERT: B 128 VAL cc_start: 0.7412 (t) cc_final: 0.7055 (p) REVERT: B 273 ILE cc_start: 0.7913 (mm) cc_final: 0.7535 (mm) REVERT: B 287 LEU cc_start: 0.8958 (mt) cc_final: 0.8059 (mt) REVERT: B 306 LEU cc_start: 0.9265 (mt) cc_final: 0.8612 (mm) REVERT: B 877 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6353 (mt-10) REVERT: C 273 ILE cc_start: 0.7913 (mm) cc_final: 0.7579 (mm) REVERT: C 287 LEU cc_start: 0.9070 (mt) cc_final: 0.8100 (mt) REVERT: C 306 LEU cc_start: 0.9228 (mt) cc_final: 0.8587 (mm) REVERT: D 128 VAL cc_start: 0.7847 (t) cc_final: 0.7487 (p) REVERT: D 273 ILE cc_start: 0.7999 (mm) cc_final: 0.7702 (mm) REVERT: D 287 LEU cc_start: 0.8995 (mt) cc_final: 0.8093 (mt) REVERT: D 306 LEU cc_start: 0.9234 (mt) cc_final: 0.8614 (mm) REVERT: D 901 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7564 (ttmt) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.3120 time to fit residues: 185.8404 Evaluate side-chains 206 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.0770 chunk 63 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS B 308 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 308 ASN ** C 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10176 Z= 0.217 Angle : 0.751 7.657 13704 Z= 0.389 Chirality : 0.040 0.127 1540 Planarity : 0.004 0.033 1792 Dihedral : 6.157 20.842 1376 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 1.65 % Allowed : 14.38 % Favored : 83.97 % 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: -1.77 (0.22), residues: 1248 helix: -0.04 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -3.75 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 248 PHE 0.018 0.002 PHE A 251 TYR 0.023 0.002 TYR D 231 ARG 0.008 0.001 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 241 time to evaluate : 1.334 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: symmetry clash REVERT: A 149 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: A 277 LYS cc_start: 0.8367 (mmpt) cc_final: 0.7903 (mmpt) REVERT: A 285 LEU cc_start: 0.9324 (mm) cc_final: 0.8937 (pt) REVERT: A 288 SER cc_start: 0.8765 (p) cc_final: 0.8255 (p) REVERT: A 872 ASP cc_start: 0.8825 (t0) cc_final: 0.8621 (t70) REVERT: A 911 LEU cc_start: 0.8691 (tt) cc_final: 0.8383 (mt) REVERT: B 128 VAL cc_start: 0.7245 (t) cc_final: 0.6989 (p) REVERT: B 298 GLU cc_start: 0.7919 (tt0) cc_final: 0.7657 (tt0) REVERT: B 876 ASP cc_start: 0.8453 (p0) cc_final: 0.8225 (p0) REVERT: B 877 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6699 (mt-10) REVERT: B 911 LEU cc_start: 0.8224 (tt) cc_final: 0.7983 (mm) REVERT: C 128 VAL cc_start: 0.7376 (t) cc_final: 0.7101 (p) REVERT: C 298 GLU cc_start: 0.7993 (tt0) cc_final: 0.7725 (tt0) REVERT: D 128 VAL cc_start: 0.7570 (t) cc_final: 0.7312 (p) REVERT: D 229 GLN cc_start: 0.8931 (mp10) cc_final: 0.8634 (mp10) REVERT: D 277 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7996 (mppt) outliers start: 18 outliers final: 12 residues processed: 250 average time/residue: 0.2036 time to fit residues: 71.6992 Evaluate side-chains 199 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 876 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 GLN A 227 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 HIS ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10176 Z= 0.243 Angle : 0.700 7.531 13704 Z= 0.363 Chirality : 0.040 0.129 1540 Planarity : 0.004 0.031 1792 Dihedral : 5.678 23.331 1376 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.56 % Allowed : 16.94 % Favored : 80.49 % 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: -0.72 (0.23), residues: 1248 helix: 0.89 (0.17), residues: 852 sheet: None (None), residues: 0 loop : -3.70 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 227 PHE 0.017 0.001 PHE B 251 TYR 0.023 0.002 TYR D 231 ARG 0.005 0.001 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.123 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 VAL cc_start: 0.8155 (t) cc_final: 0.7916 (p) REVERT: A 149 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: A 285 LEU cc_start: 0.9294 (mm) cc_final: 0.8994 (pt) REVERT: A 911 LEU cc_start: 0.8865 (tt) cc_final: 0.8502 (mt) REVERT: B 252 CYS cc_start: 0.9442 (t) cc_final: 0.9212 (t) REVERT: B 277 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7885 (mmtm) REVERT: B 911 LEU cc_start: 0.8393 (tt) cc_final: 0.7841 (mt) REVERT: C 251 PHE cc_start: 0.6564 (t80) cc_final: 0.6285 (t80) REVERT: C 274 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8529 (m-40) REVERT: C 298 GLU cc_start: 0.7971 (tt0) cc_final: 0.7659 (tt0) REVERT: C 858 MET cc_start: 0.8963 (mmm) cc_final: 0.8751 (mmm) REVERT: C 911 LEU cc_start: 0.8431 (tt) cc_final: 0.8124 (mt) REVERT: D 252 CYS cc_start: 0.9465 (t) cc_final: 0.9252 (t) REVERT: D 911 LEU cc_start: 0.8660 (tt) cc_final: 0.8400 (mm) outliers start: 28 outliers final: 17 residues processed: 206 average time/residue: 0.2082 time to fit residues: 60.7790 Evaluate side-chains 187 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS C 217 HIS ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10176 Z= 0.222 Angle : 0.663 7.361 13704 Z= 0.346 Chirality : 0.039 0.157 1540 Planarity : 0.003 0.035 1792 Dihedral : 5.496 23.177 1376 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.20 % Allowed : 18.68 % Favored : 79.12 % 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: -0.14 (0.24), residues: 1248 helix: 1.39 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.70 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 235 PHE 0.018 0.001 PHE B 251 TYR 0.020 0.002 TYR D 231 ARG 0.004 0.001 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 1.144 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: A 149 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: A 153 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8657 (mtpp) REVERT: A 285 LEU cc_start: 0.9313 (mm) cc_final: 0.8873 (pt) REVERT: A 900 GLU cc_start: 0.7995 (tt0) cc_final: 0.7444 (tt0) REVERT: A 911 LEU cc_start: 0.8790 (tt) cc_final: 0.8395 (mt) REVERT: B 277 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8025 (mmtm) REVERT: B 298 GLU cc_start: 0.7917 (tt0) cc_final: 0.7507 (tt0) REVERT: B 858 MET cc_start: 0.9050 (mmm) cc_final: 0.8836 (mmm) REVERT: B 911 LEU cc_start: 0.8384 (tt) cc_final: 0.7904 (mt) REVERT: C 128 VAL cc_start: 0.7946 (t) cc_final: 0.7675 (p) REVERT: C 149 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 201 GLN cc_start: 0.5565 (pm20) cc_final: 0.5299 (pm20) REVERT: C 251 PHE cc_start: 0.6527 (t80) cc_final: 0.6253 (t80) REVERT: C 298 GLU cc_start: 0.8008 (tt0) cc_final: 0.7714 (tt0) REVERT: C 858 MET cc_start: 0.8921 (mmm) cc_final: 0.8713 (mmm) REVERT: C 900 GLU cc_start: 0.6942 (tp30) cc_final: 0.6691 (tp30) REVERT: C 911 LEU cc_start: 0.8427 (tt) cc_final: 0.7976 (mt) REVERT: D 229 GLN cc_start: 0.8969 (mp10) cc_final: 0.8741 (mp10) REVERT: D 277 LYS cc_start: 0.8777 (mmpt) cc_final: 0.8557 (mmtm) REVERT: D 285 LEU cc_start: 0.9323 (mm) cc_final: 0.8961 (pt) REVERT: D 312 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7705 (mp0) outliers start: 24 outliers final: 14 residues processed: 194 average time/residue: 0.2152 time to fit residues: 58.8045 Evaluate side-chains 180 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 288 SER Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN B 855 GLN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 227 HIS C 855 GLN D 144 HIS ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10176 Z= 0.380 Angle : 0.764 8.252 13704 Z= 0.399 Chirality : 0.043 0.158 1540 Planarity : 0.004 0.045 1792 Dihedral : 5.560 24.292 1376 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.11 % Allowed : 20.60 % Favored : 76.28 % 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: -0.22 (0.25), residues: 1248 helix: 1.30 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -4.03 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 144 PHE 0.027 0.002 PHE A 215 TYR 0.026 0.002 TYR A 231 ARG 0.007 0.001 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8884 (mtpp) REVERT: A 285 LEU cc_start: 0.9364 (mm) cc_final: 0.8948 (pt) REVERT: A 900 GLU cc_start: 0.8083 (tt0) cc_final: 0.7309 (tt0) REVERT: B 267 SER cc_start: 0.8770 (t) cc_final: 0.8481 (p) REVERT: B 298 GLU cc_start: 0.8255 (tt0) cc_final: 0.7832 (tt0) REVERT: B 911 LEU cc_start: 0.8602 (tt) cc_final: 0.8264 (mm) REVERT: C 251 PHE cc_start: 0.6660 (t80) cc_final: 0.6371 (t80) REVERT: C 298 GLU cc_start: 0.8205 (tt0) cc_final: 0.7782 (tt0) REVERT: C 911 LEU cc_start: 0.8664 (tt) cc_final: 0.8118 (mt) REVERT: D 229 GLN cc_start: 0.8991 (mp10) cc_final: 0.8736 (mp10) REVERT: D 277 LYS cc_start: 0.8785 (mmpt) cc_final: 0.8521 (mmpt) REVERT: D 285 LEU cc_start: 0.9370 (mm) cc_final: 0.8962 (pt) REVERT: D 312 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7812 (mp0) REVERT: D 320 LEU cc_start: 0.8300 (mt) cc_final: 0.8099 (mt) REVERT: D 900 GLU cc_start: 0.7260 (tp30) cc_final: 0.6996 (tp30) outliers start: 34 outliers final: 20 residues processed: 206 average time/residue: 0.2119 time to fit residues: 61.5245 Evaluate side-chains 183 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 CYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 250 TYR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.1980 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10176 Z= 0.200 Angle : 0.690 9.751 13704 Z= 0.357 Chirality : 0.040 0.211 1540 Planarity : 0.003 0.035 1792 Dihedral : 5.475 24.787 1376 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.29 % Allowed : 21.98 % Favored : 75.73 % 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: 0.08 (0.25), residues: 1248 helix: 1.55 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.92 (0.25), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 144 PHE 0.024 0.002 PHE C 215 TYR 0.023 0.002 TYR A 231 ARG 0.003 0.001 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8846 (mtpp) REVERT: A 285 LEU cc_start: 0.9322 (mm) cc_final: 0.8888 (pt) REVERT: A 900 GLU cc_start: 0.8069 (tt0) cc_final: 0.7280 (tt0) REVERT: B 149 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 177 GLU cc_start: 0.8081 (tp30) cc_final: 0.7690 (tp30) REVERT: B 877 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6069 (mm-30) REVERT: C 128 VAL cc_start: 0.8085 (t) cc_final: 0.7828 (p) REVERT: C 177 GLU cc_start: 0.8133 (tp30) cc_final: 0.7744 (tp30) REVERT: C 251 PHE cc_start: 0.6533 (t80) cc_final: 0.6263 (t80) REVERT: C 285 LEU cc_start: 0.9363 (mm) cc_final: 0.9046 (pt) REVERT: C 298 GLU cc_start: 0.8107 (tt0) cc_final: 0.7764 (tt0) REVERT: C 900 GLU cc_start: 0.7882 (tt0) cc_final: 0.7646 (tt0) REVERT: C 911 LEU cc_start: 0.8387 (tt) cc_final: 0.8064 (mt) REVERT: D 128 VAL cc_start: 0.8241 (t) cc_final: 0.7959 (p) REVERT: D 229 GLN cc_start: 0.8984 (mp10) cc_final: 0.8664 (mp10) REVERT: D 285 LEU cc_start: 0.9206 (mm) cc_final: 0.8718 (pt) REVERT: D 312 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7565 (mp0) REVERT: D 911 LEU cc_start: 0.8472 (tt) cc_final: 0.8212 (mm) outliers start: 25 outliers final: 13 residues processed: 192 average time/residue: 0.2000 time to fit residues: 55.0240 Evaluate side-chains 174 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 0.0060 chunk 72 optimal weight: 0.0010 chunk 55 optimal weight: 0.6980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10176 Z= 0.195 Angle : 0.673 10.262 13704 Z= 0.347 Chirality : 0.040 0.204 1540 Planarity : 0.003 0.035 1792 Dihedral : 5.350 24.216 1376 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.38 % Allowed : 21.98 % Favored : 75.64 % 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: 0.20 (0.25), residues: 1248 helix: 1.65 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -3.91 (0.25), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 144 PHE 0.022 0.001 PHE A 215 TYR 0.038 0.002 TYR D 231 ARG 0.003 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: A 153 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8455 (mtpp) REVERT: A 285 LEU cc_start: 0.9304 (mm) cc_final: 0.8876 (pt) REVERT: B 285 LEU cc_start: 0.9379 (mm) cc_final: 0.9026 (pt) REVERT: B 298 GLU cc_start: 0.8239 (tt0) cc_final: 0.7890 (tt0) REVERT: B 312 GLU cc_start: 0.7647 (mp0) cc_final: 0.7161 (mp0) REVERT: B 872 ASP cc_start: 0.8718 (t0) cc_final: 0.8480 (t70) REVERT: C 128 VAL cc_start: 0.8176 (t) cc_final: 0.7972 (p) REVERT: C 285 LEU cc_start: 0.9380 (mm) cc_final: 0.9033 (pt) REVERT: C 298 GLU cc_start: 0.8151 (tt0) cc_final: 0.7794 (tt0) REVERT: C 872 ASP cc_start: 0.8809 (t0) cc_final: 0.8559 (t70) REVERT: C 887 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8465 (mmmm) REVERT: C 900 GLU cc_start: 0.7982 (tt0) cc_final: 0.7739 (tt0) REVERT: C 911 LEU cc_start: 0.8339 (tt) cc_final: 0.8116 (mt) REVERT: D 128 VAL cc_start: 0.8168 (t) cc_final: 0.7914 (p) REVERT: D 285 LEU cc_start: 0.9166 (mm) cc_final: 0.8805 (pt) REVERT: D 312 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7775 (mp0) REVERT: D 872 ASP cc_start: 0.8848 (t0) cc_final: 0.8563 (t70) REVERT: D 911 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8193 (mm) outliers start: 26 outliers final: 11 residues processed: 197 average time/residue: 0.2161 time to fit residues: 59.4856 Evaluate side-chains 182 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 288 SER Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 887 LYS Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 911 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10176 Z= 0.209 Angle : 0.697 10.871 13704 Z= 0.362 Chirality : 0.041 0.179 1540 Planarity : 0.004 0.045 1792 Dihedral : 5.293 24.155 1376 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 1.74 % Allowed : 23.26 % Favored : 75.00 % 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: 0.20 (0.25), residues: 1248 helix: 1.63 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -3.92 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 227 PHE 0.030 0.002 PHE B 215 TYR 0.044 0.002 TYR D 231 ARG 0.004 0.000 ARG D 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 153 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8517 (mtpp) REVERT: A 285 LEU cc_start: 0.9322 (mm) cc_final: 0.8894 (pt) REVERT: A 322 MET cc_start: 0.9140 (mmm) cc_final: 0.8938 (mmm) REVERT: A 900 GLU cc_start: 0.8099 (tt0) cc_final: 0.7784 (tt0) REVERT: B 177 GLU cc_start: 0.8071 (tp30) cc_final: 0.7698 (tp30) REVERT: B 285 LEU cc_start: 0.9391 (mm) cc_final: 0.9020 (pt) REVERT: B 298 GLU cc_start: 0.8129 (tt0) cc_final: 0.7732 (tt0) REVERT: C 177 GLU cc_start: 0.8139 (tp30) cc_final: 0.7757 (tp30) REVERT: C 285 LEU cc_start: 0.9394 (mm) cc_final: 0.8977 (pt) REVERT: C 298 GLU cc_start: 0.8111 (tt0) cc_final: 0.7652 (tt0) REVERT: C 872 ASP cc_start: 0.8818 (t0) cc_final: 0.8542 (t70) REVERT: C 887 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8496 (mmmm) REVERT: C 900 GLU cc_start: 0.7918 (tt0) cc_final: 0.7622 (tt0) REVERT: C 911 LEU cc_start: 0.8428 (tt) cc_final: 0.8097 (mt) REVERT: D 128 VAL cc_start: 0.8186 (t) cc_final: 0.7955 (p) REVERT: D 285 LEU cc_start: 0.9218 (mm) cc_final: 0.8724 (pt) REVERT: D 312 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7549 (mp0) REVERT: D 872 ASP cc_start: 0.8853 (t0) cc_final: 0.8577 (t70) REVERT: D 911 LEU cc_start: 0.8461 (tt) cc_final: 0.8229 (mm) outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 0.2087 time to fit residues: 53.5288 Evaluate side-chains 174 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 161 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 887 LYS Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10176 Z= 0.230 Angle : 0.698 10.819 13704 Z= 0.362 Chirality : 0.041 0.169 1540 Planarity : 0.003 0.032 1792 Dihedral : 5.193 24.173 1376 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.11 % Allowed : 23.08 % Favored : 74.82 % 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: 0.22 (0.25), residues: 1248 helix: 1.65 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -3.95 (0.25), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 227 PHE 0.028 0.002 PHE B 215 TYR 0.019 0.002 TYR A 231 ARG 0.003 0.000 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: A 153 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8532 (mtpp) REVERT: A 285 LEU cc_start: 0.9345 (mm) cc_final: 0.8918 (pt) REVERT: A 320 LEU cc_start: 0.8357 (mt) cc_final: 0.8100 (mt) REVERT: A 900 GLU cc_start: 0.8140 (tt0) cc_final: 0.7781 (tt0) REVERT: B 285 LEU cc_start: 0.9401 (mm) cc_final: 0.9024 (pt) REVERT: B 298 GLU cc_start: 0.8195 (tt0) cc_final: 0.7786 (tt0) REVERT: B 312 GLU cc_start: 0.7654 (mp0) cc_final: 0.7374 (mp0) REVERT: C 177 GLU cc_start: 0.8207 (tp30) cc_final: 0.7799 (tp30) REVERT: C 285 LEU cc_start: 0.9312 (mm) cc_final: 0.8841 (pt) REVERT: C 298 GLU cc_start: 0.8130 (tt0) cc_final: 0.7697 (tt0) REVERT: C 872 ASP cc_start: 0.8829 (t0) cc_final: 0.8610 (t70) REVERT: C 887 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8521 (mmmm) REVERT: C 900 GLU cc_start: 0.7915 (tt0) cc_final: 0.7714 (tt0) REVERT: C 911 LEU cc_start: 0.8451 (tt) cc_final: 0.8096 (mt) REVERT: D 231 TYR cc_start: 0.8263 (t80) cc_final: 0.8032 (t80) REVERT: D 267 SER cc_start: 0.9045 (t) cc_final: 0.8761 (p) REVERT: D 285 LEU cc_start: 0.9246 (mm) cc_final: 0.8654 (pt) REVERT: D 312 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7760 (mp0) REVERT: D 872 ASP cc_start: 0.8870 (t0) cc_final: 0.8606 (t70) REVERT: D 911 LEU cc_start: 0.8630 (tt) cc_final: 0.8389 (mm) outliers start: 23 outliers final: 15 residues processed: 196 average time/residue: 0.2021 time to fit residues: 56.9402 Evaluate side-chains 182 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 887 LYS Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10176 Z= 0.211 Angle : 0.716 11.262 13704 Z= 0.360 Chirality : 0.041 0.168 1540 Planarity : 0.003 0.032 1792 Dihedral : 5.179 24.066 1376 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 1.65 % Allowed : 23.90 % Favored : 74.45 % 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: 0.24 (0.25), residues: 1248 helix: 1.68 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -3.97 (0.25), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 144 PHE 0.028 0.001 PHE B 215 TYR 0.019 0.002 TYR A 231 ARG 0.002 0.000 ARG A 894 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: A 153 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8563 (mtpp) REVERT: A 285 LEU cc_start: 0.9339 (mm) cc_final: 0.8892 (pt) REVERT: A 320 LEU cc_start: 0.8336 (mt) cc_final: 0.8093 (mt) REVERT: A 900 GLU cc_start: 0.8120 (tt0) cc_final: 0.7785 (tt0) REVERT: B 177 GLU cc_start: 0.8110 (tp30) cc_final: 0.7751 (tp30) REVERT: B 230 GLU cc_start: 0.7766 (mp0) cc_final: 0.6829 (mp0) REVERT: B 285 LEU cc_start: 0.9402 (mm) cc_final: 0.9014 (pt) REVERT: B 298 GLU cc_start: 0.8167 (tt0) cc_final: 0.7784 (tt0) REVERT: B 312 GLU cc_start: 0.7844 (mp0) cc_final: 0.7508 (mp0) REVERT: B 319 LYS cc_start: 0.7632 (tttt) cc_final: 0.7068 (tppt) REVERT: C 177 GLU cc_start: 0.8198 (tp30) cc_final: 0.7789 (tp30) REVERT: C 285 LEU cc_start: 0.9241 (mm) cc_final: 0.8781 (pt) REVERT: C 298 GLU cc_start: 0.8163 (tt0) cc_final: 0.7852 (tt0) REVERT: C 887 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8490 (mmmm) REVERT: C 900 GLU cc_start: 0.7921 (tt0) cc_final: 0.7717 (tt0) REVERT: C 911 LEU cc_start: 0.8416 (tt) cc_final: 0.8089 (mt) REVERT: D 267 SER cc_start: 0.9091 (t) cc_final: 0.8781 (p) REVERT: D 285 LEU cc_start: 0.9258 (mm) cc_final: 0.8727 (pt) REVERT: D 312 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7669 (mp0) REVERT: D 872 ASP cc_start: 0.8836 (t0) cc_final: 0.8582 (t70) REVERT: D 911 LEU cc_start: 0.8594 (tt) cc_final: 0.8357 (mm) outliers start: 18 outliers final: 11 residues processed: 172 average time/residue: 0.1961 time to fit residues: 48.9723 Evaluate side-chains 170 residues out of total 1128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 127 CYS Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 127 CYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 887 LYS Chi-restraints excluded: chain D residue 127 CYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.098214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082311 restraints weight = 31496.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.084744 restraints weight = 18621.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086396 restraints weight = 13022.325| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10176 Z= 0.213 Angle : 0.717 10.823 13704 Z= 0.363 Chirality : 0.042 0.167 1540 Planarity : 0.003 0.032 1792 Dihedral : 5.139 23.860 1376 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.10 % Allowed : 24.54 % Favored : 74.36 % 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: 0.25 (0.25), residues: 1248 helix: 1.69 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -3.98 (0.25), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 144 PHE 0.028 0.001 PHE B 215 TYR 0.019 0.002 TYR A 231 ARG 0.002 0.000 ARG A 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.98 seconds wall clock time: 40 minutes 29.12 seconds (2429.12 seconds total)