Starting phenix.real_space_refine (version: dev) on Sat Feb 18 11:29:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6q_12740/02_2023/7o6q_12740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6q_12740/02_2023/7o6q_12740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6q_12740/02_2023/7o6q_12740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6q_12740/02_2023/7o6q_12740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6q_12740/02_2023/7o6q_12740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6q_12740/02_2023/7o6q_12740.pdb" } resolution = 1.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.042 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 Process input model Symmetric amino acids flipped Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7999 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1902 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1813 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 248, 1813 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 bond proxies already assigned to first conformer: 1736 Chain: "B" Number of atoms: 1879 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1813 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 248, 1813 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 4, 'TRANS': 243} Chain breaks: 1 bond proxies already assigned to first conformer: 1762 Chain: "C" Number of atoms: 1917 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 1836 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 1836 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 1768 Chain: "D" Number of atoms: 1902 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 1830 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 250, 1830 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 bond proxies already assigned to first conformer: 1772 Chain: "A" Number of atoms: 101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Conformer: "B" Number of residues, atoms: 95, 95 Classifications: {'water': 95} Link IDs: {None: 94} Chain: "B" Number of atoms: 96 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Conformer: "B" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "C" Number of atoms: 103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Conformer: "B" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "D" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Conformer: "B" Number of residues, atoms: 97, 97 Classifications: {'water': 97} Link IDs: {None: 96} Residues with excluded nonbonded symmetry interactions: 61 residue: pdb=" N AARG A 58 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 58 " occ=0.50 residue: pdb=" N ASER A 61 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 61 " occ=0.50 residue: pdb=" N AASP A 71 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 71 " occ=0.50 residue: pdb=" N AARG A 74 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 74 " occ=0.50 residue: pdb=" N AGLU A 98 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 98 " occ=0.50 residue: pdb=" N APHE A 104 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 104 " occ=0.50 residue: pdb=" N ALYS A 137 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 137 " occ=0.50 residue: pdb=" N ASER A 179 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 179 " occ=0.50 residue: pdb=" N AGLU A 225 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 225 " occ=0.50 residue: pdb=" N AGLU A 237 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 237 " occ=0.50 residue: pdb=" N AARG B 58 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.50 residue: pdb=" N AARG B 74 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 74 " occ=0.50 ... (remaining 49 not shown) Time building chain proxies: 8.45, per 1000 atoms: 1.06 Number of scatterers: 7999 At special positions: 0 Unit cell: (75.555, 92.637, 82.782, 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 40 16.00 O 1859 8.00 N 1323 7.00 C 4777 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: 3.29 Conformation dependent library (CDL) restraints added in 2.4 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 61.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.722A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 156 through 179 removed outlier: 3.900A pdb=" N ASER A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 223 through 236 removed outlier: 3.514A pdb=" N VAL A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 removed outlier: 3.551A pdb=" N SER A 240 " --> pdb=" O AGLU A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 237 through 240' Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.659A pdb=" N VAL A 256 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.733A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 85 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 156 through 179 removed outlier: 3.899A pdb=" N ASER B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 223 through 236 removed outlier: 3.516A pdb=" N VAL B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 240 removed outlier: 3.546A pdb=" N SER B 240 " --> pdb=" O AGLU B 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 240' Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.659A pdb=" N VAL B 256 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.666A pdb=" N GLY B 267 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.760A pdb=" N GLY C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 85 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 119 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 156 through 179 removed outlier: 3.900A pdb=" N ASER C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 215 Processing helix chain 'C' and resid 223 through 236 Processing helix chain 'C' and resid 237 through 240 removed outlier: 3.548A pdb=" N SER C 240 " --> pdb=" O AGLU C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 240' Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.658A pdb=" N VAL C 256 " --> pdb=" O TYR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.717A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 85 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 119 through 134 Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 156 through 179 removed outlier: 3.924A pdb=" N SER D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 215 removed outlier: 3.566A pdb=" N GLY D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 236 removed outlier: 3.550A pdb=" N VAL D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 240 removed outlier: 3.548A pdb=" N SER D 240 " --> pdb=" O AGLU D 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 237 through 240' Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.658A pdb=" N VAL D 256 " --> pdb=" O TYR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64 removed outlier: 3.554A pdb=" N ASP A 43 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 14 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE A 91 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 16 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET A 90 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR A 144 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N SER A 92 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N LEU A 247 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS A 186 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A 249 " --> pdb=" O CYS A 186 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER A 188 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 64 removed outlier: 3.549A pdb=" N ASP B 43 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 14 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE B 91 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 16 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET B 90 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR B 144 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER B 92 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 60 through 64 removed outlier: 6.548A pdb=" N VAL C 39 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR C 63 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE C 41 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 14 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE C 91 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE C 16 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N MET C 90 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR C 144 " --> pdb=" O MET C 90 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SER C 92 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU C 247 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N CYS C 186 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL C 249 " --> pdb=" O CYS C 186 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 188 " --> pdb=" O VAL C 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 60 through 64 removed outlier: 3.539A pdb=" N ASP D 43 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 14 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N PHE D 91 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE D 16 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET D 90 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N THR D 144 " --> pdb=" O MET D 90 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER D 92 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU D 247 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS D 186 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL D 249 " --> pdb=" O CYS D 186 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER D 188 " --> pdb=" O VAL D 249 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1327 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: 2.55 Time building geometry restraints manager: 3.52 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: 2501 1.33 - 1.45: 897 1.45 - 1.57: 4268 1.57 - 1.69: 0 1.69 - 1.80: 64 Bond restraints: 7730 Sorted by residual: bond pdb=" CB CYS B 140 " pdb=" SG CYS B 140 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.09e+00 bond pdb=" CB CYS C 140 " pdb=" SG CYS C 140 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.79e+00 bond pdb=" CB THR A 28 " pdb=" CG2 THR A 28 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " ideal model delta sigma weight residual 1.808 1.762 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CB THR D 28 " pdb=" CG2 THR D 28 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 ... (remaining 7725 not shown) Histogram of bond angle deviations from ideal: 99.30 - 105.72: 73 105.72 - 112.13: 3885 112.13 - 118.55: 2154 118.55 - 124.96: 4335 124.96 - 131.38: 49 Bond angle restraints: 10496 Sorted by residual: angle pdb=" C ALA D 136 " pdb=" N BLYS D 137 " pdb=" CA BLYS D 137 " ideal model delta sigma weight residual 122.74 127.91 -5.17 1.44e+00 4.82e-01 1.29e+01 angle pdb=" C ALA B 136 " pdb=" N LYS B 137 " pdb=" CA LYS B 137 " ideal model delta sigma weight residual 122.74 127.52 -4.78 1.44e+00 4.82e-01 1.10e+01 angle pdb=" C ALA C 136 " pdb=" N LYS C 137 " pdb=" CA LYS C 137 " ideal model delta sigma weight residual 122.74 126.89 -4.15 1.44e+00 4.82e-01 8.30e+00 angle pdb=" C MET A 133 " pdb=" N VAL A 134 " pdb=" CA VAL A 134 " ideal model delta sigma weight residual 120.43 122.87 -2.44 9.60e-01 1.09e+00 6.46e+00 angle pdb=" C MET D 133 " pdb=" N VAL D 134 " pdb=" CA VAL D 134 " ideal model delta sigma weight residual 120.43 122.77 -2.34 9.60e-01 1.09e+00 5.93e+00 ... (remaining 10491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 4246 16.61 - 33.23: 284 33.23 - 49.84: 49 49.84 - 66.45: 15 66.45 - 83.07: 10 Dihedral angle restraints: 4604 sinusoidal: 1693 harmonic: 2911 Sorted by residual: dihedral pdb=" CA VAL A 256 " pdb=" C VAL A 256 " pdb=" N ASN A 257 " pdb=" CA ASN A 257 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA VAL D 256 " pdb=" C VAL D 256 " pdb=" N ASN D 257 " pdb=" CA ASN D 257 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA VAL C 256 " pdb=" C VAL C 256 " pdb=" N ASN C 257 " pdb=" CA ASN C 257 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 4601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 482 0.030 - 0.060: 428 0.060 - 0.090: 200 0.090 - 0.120: 89 0.120 - 0.150: 39 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CA BLYS D 137 " pdb=" N BLYS D 137 " pdb=" C BLYS D 137 " pdb=" CB BLYS D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA LYS B 137 " pdb=" N LYS B 137 " pdb=" C LYS B 137 " pdb=" CB LYS B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA HIS B 128 " pdb=" N HIS B 128 " pdb=" C HIS B 128 " pdb=" CB HIS B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 1235 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 128 " -0.019 2.00e-02 2.50e+03 1.72e-02 4.46e+00 pdb=" CG HIS B 128 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 128 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 128 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 128 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS B 128 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 128 " -0.019 2.00e-02 2.50e+03 1.72e-02 4.44e+00 pdb=" CG HIS D 128 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS D 128 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 128 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS D 128 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS D 128 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 128 " 0.019 2.00e-02 2.50e+03 1.70e-02 4.35e+00 pdb=" CG HIS A 128 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 128 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 128 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 128 " 0.004 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 311 2.67 - 3.23: 8219 3.23 - 3.79: 13899 3.79 - 4.34: 20514 4.34 - 4.90: 31143 Nonbonded interactions: 74086 Sorted by model distance: nonbonded pdb=" OD2 ASP A 43 " pdb=" O HOH A 301 " model vdw 2.115 2.440 nonbonded pdb=" OD2 ASP D 43 " pdb=" O HOH D 301 " model vdw 2.115 2.440 nonbonded pdb=" OE2 GLU C 98 " pdb=" O HOH C 301 " model vdw 2.121 2.440 nonbonded pdb=" OG BSER A 61 " pdb=" O HOH A 302 " model vdw 2.172 2.440 nonbonded pdb=" OD1 ASN C 59 " pdb=" O HOH C 302 " model vdw 2.179 2.440 ... (remaining 74081 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 8 through 57 or resid 59 through 60 or resid 62 through 70 \ or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid \ 105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ hrough 178 or resid 180 through 186 or resid 188 through 224 or resid 226 throug \ h 236 or resid 238 through 268)) selection = (chain 'B' and (resid 8 through 57 or resid 59 through 60 or resid 62 through 70 \ or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid \ 105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ hrough 178 or resid 180 through 186 or resid 188 through 224 or resid 226 throug \ h 236 or resid 238 through 268)) selection = (chain 'C' and (resid 8 through 57 or resid 59 through 60 or resid 62 through 70 \ or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid \ 105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ hrough 178 or resid 180 through 186 or resid 188 through 192 or resid 206 throug \ h 224 or resid 226 through 236 or resid 238 through 268)) selection = (chain 'D' and (resid 8 through 57 or resid 59 through 60 or resid 62 through 70 \ or resid 72 through 73 or resid 75 through 97 or resid 99 through 103 or resid \ 105 through 109 or resid 111 through 136 or resid 138 through 171 or resid 173 t \ hrough 178 or resid 180 through 186 or resid 188 through 192 or resid 206 throug \ h 224 or resid 226 through 236 or resid 238 through 268)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4777 2.51 5 N 1323 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=0.96 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: 4.270 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: 12.800 Check model and map are aligned: 0.130 Process input model: 30.210 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.010 0.061 7730 Z= 0.640 Angle : 0.708 5.648 10496 Z= 0.398 Chirality : 0.055 0.150 1238 Planarity : 0.006 0.045 1374 Dihedral : 12.799 83.066 2774 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.25 % 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 (0.23), residues: 1083 helix: -1.25 (0.19), residues: 528 sheet: -0.75 (0.36), residues: 177 loop : -0.58 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.890 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 1.8721 time to fit residues: 249.2050 Evaluate side-chains 104 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 102 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.1091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7730 Z= 0.195 Angle : 0.497 4.637 10496 Z= 0.280 Chirality : 0.042 0.146 1238 Planarity : 0.004 0.027 1374 Dihedral : 4.784 18.279 1125 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.50 % 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: 1.34 (0.26), residues: 1083 helix: 1.44 (0.22), residues: 538 sheet: 0.06 (0.41), residues: 173 loop : 0.72 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.930 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 116 average time/residue: 1.9980 time to fit residues: 240.8356 Evaluate side-chains 106 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 1 average time/residue: 0.1237 time to fit residues: 1.4528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 93 ASN D 45 GLN D 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 7730 Z= 0.313 Angle : 0.520 4.663 10496 Z= 0.292 Chirality : 0.044 0.144 1238 Planarity : 0.003 0.025 1374 Dihedral : 4.748 18.757 1125 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.50 % 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 (0.27), residues: 1083 helix: 2.02 (0.22), residues: 538 sheet: -0.11 (0.40), residues: 176 loop : 1.10 (0.36), residues: 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.923 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 108 average time/residue: 1.9254 time to fit residues: 216.6237 Evaluate side-chains 107 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.1186 time to fit residues: 1.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7730 Z= 0.180 Angle : 0.453 7.166 10496 Z= 0.252 Chirality : 0.042 0.135 1238 Planarity : 0.003 0.022 1374 Dihedral : 4.420 17.127 1125 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.50 % 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: 2.55 (0.27), residues: 1083 helix: 2.58 (0.22), residues: 538 sheet: 0.07 (0.41), residues: 173 loop : 1.36 (0.38), residues: 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.870 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 119 average time/residue: 1.8742 time to fit residues: 232.8650 Evaluate side-chains 113 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.1472 time to fit residues: 1.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 70 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 7730 Z= 0.258 Angle : 0.482 5.246 10496 Z= 0.269 Chirality : 0.042 0.137 1238 Planarity : 0.003 0.022 1374 Dihedral : 4.491 17.825 1125 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 1.25 % 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: 2.64 (0.27), residues: 1083 helix: 2.65 (0.22), residues: 538 sheet: 0.10 (0.41), residues: 173 loop : 1.41 (0.38), residues: 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.832 Fit side-chains outliers start: 5 outliers final: 6 residues processed: 111 average time/residue: 2.0004 time to fit residues: 231.6085 Evaluate side-chains 111 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.261 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.2384 time to fit residues: 2.0696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.4980 chunk 18 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7730 Z= 0.177 Angle : 0.437 5.319 10496 Z= 0.243 Chirality : 0.041 0.132 1238 Planarity : 0.002 0.021 1374 Dihedral : 4.270 16.746 1125 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.25 % 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: 2.90 (0.28), residues: 1083 helix: 2.93 (0.22), residues: 539 sheet: 0.09 (0.41), residues: 173 loop : 1.49 (0.38), residues: 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.917 Fit side-chains outliers start: 5 outliers final: 6 residues processed: 113 average time/residue: 1.8391 time to fit residues: 216.8264 Evaluate side-chains 111 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 1 average time/residue: 0.1149 time to fit residues: 1.4233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 7730 Z= 0.194 Angle : 0.440 4.649 10496 Z= 0.245 Chirality : 0.041 0.132 1238 Planarity : 0.002 0.021 1374 Dihedral : 4.246 16.559 1125 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.38 % 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: 3.02 (0.28), residues: 1083 helix: 2.99 (0.22), residues: 541 sheet: 0.12 (0.41), residues: 173 loop : 1.63 (0.39), residues: 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.903 Fit side-chains outliers start: 6 outliers final: 7 residues processed: 109 average time/residue: 1.9667 time to fit residues: 223.2587 Evaluate side-chains 111 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 2 average time/residue: 0.1156 time to fit residues: 1.4261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 85 optimal weight: 0.0050 chunk 90 optimal weight: 1.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 7730 Z= 0.139 Angle : 0.410 4.627 10496 Z= 0.228 Chirality : 0.040 0.129 1238 Planarity : 0.002 0.020 1374 Dihedral : 4.050 15.208 1125 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 1.50 % 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: 3.22 (0.28), residues: 1083 helix: 3.18 (0.22), residues: 541 sheet: 0.14 (0.42), residues: 173 loop : 1.72 (0.39), residues: 369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.911 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 114 average time/residue: 1.9288 time to fit residues: 229.3302 Evaluate side-chains 114 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 2 average time/residue: 0.1256 time to fit residues: 1.6286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7730 Z= 0.212 Angle : 0.444 4.694 10496 Z= 0.247 Chirality : 0.041 0.134 1238 Planarity : 0.002 0.021 1374 Dihedral : 4.216 16.480 1125 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.38 % 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: 3.16 (0.28), residues: 1083 helix: 3.11 (0.22), residues: 541 sheet: 0.15 (0.42), residues: 173 loop : 1.71 (0.39), residues: 369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.817 Fit side-chains outliers start: 6 outliers final: 8 residues processed: 110 average time/residue: 1.9017 time to fit residues: 217.7891 Evaluate side-chains 113 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 3 average time/residue: 0.1295 time to fit residues: 1.7733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7730 Z= 0.176 Angle : 0.428 4.658 10496 Z= 0.238 Chirality : 0.041 0.132 1238 Planarity : 0.002 0.020 1374 Dihedral : 4.135 16.115 1125 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 1.38 % 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: 3.23 (0.28), residues: 1083 helix: 3.18 (0.22), residues: 541 sheet: 0.18 (0.42), residues: 173 loop : 1.73 (0.39), residues: 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.894 Fit side-chains outliers start: 6 outliers final: 8 residues processed: 113 average time/residue: 1.8922 time to fit residues: 222.6589 Evaluate side-chains 115 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 3 average time/residue: 0.1175 time to fit residues: 1.7183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.0770 chunk 14 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN D 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.110387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093955 restraints weight = 100377.514| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.57 r_work: 0.3293 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7730 Z= 0.128 Angle : 0.399 4.622 10496 Z= 0.222 Chirality : 0.040 0.128 1238 Planarity : 0.002 0.019 1374 Dihedral : 3.903 14.713 1125 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer Outliers : 1.75 % 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: 3.42 (0.28), residues: 1083 helix: 3.37 (0.22), residues: 540 sheet: 0.25 (0.42), residues: 173 loop : 1.76 (0.39), residues: 370 =============================================================================== Job complete usr+sys time: 4096.31 seconds wall clock time: 73 minutes 13.84 seconds (4393.84 seconds total)