Starting phenix.real_space_refine on Sat Jan 20 16:43:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/01_2024/7xcz_33130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/01_2024/7xcz_33130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/01_2024/7xcz_33130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/01_2024/7xcz_33130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/01_2024/7xcz_33130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/01_2024/7xcz_33130.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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: 5 Type Number sf(0) Gaussians S 30 5.16 5 C 5093 2.51 5 N 1369 2.21 5 O 1597 1.98 5 H 7747 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 105": "OD1" <-> "OD2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 216": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15836 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3023 Classifications: {'peptide': 196} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3281 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3150 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3208 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU%NH1NOTPRO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3174 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.09, per 1000 atoms: 0.45 Number of scatterers: 15836 At special positions: 0 Unit cell: (81.472, 145.792, 124.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 O 1597 8.00 N 1369 7.00 C 5093 6.00 H 7747 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 508 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 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: 12.83 Conformation dependent library (CDL) restraints added in 1.8 seconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 22 sheets defined 6.5% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.929A pdb=" N TRP A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.638A pdb=" N TYR A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.787A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.514A pdb=" N THR D 139 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.895A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.685A pdb=" N PHE C 84 " --> pdb=" O PRO C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 removed outlier: 3.503A pdb=" N LEU C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.822A pdb=" N HIS C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.536A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.536A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.010A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.767A pdb=" N ALA E 25 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.973A pdb=" N ILE E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.636A pdb=" N SER E 65 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.856A pdb=" N VAL E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.856A pdb=" N VAL E 11 " --> pdb=" O ASP E 105 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 116 through 118 removed outlier: 5.989A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.812A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 3 through 8 Processing sheet with id=AB6, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.615A pdb=" N SER B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN B 50 " --> pdb=" O TRP B 34 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TRP B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 121 through 125 removed outlier: 6.001A pdb=" N TYR B 177 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 152 through 155 removed outlier: 4.464A pdb=" N TYR B 195 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 210 " --> pdb=" O CYS B 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 13 Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.661A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 115 through 119 removed outlier: 3.668A pdb=" N VAL C 134 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 145 through 150 304 hydrogen bonds defined for protein. 759 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 13.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7747 1.03 - 1.23: 103 1.23 - 1.43: 3471 1.43 - 1.62: 4675 1.62 - 1.82: 36 Bond restraints: 16032 Sorted by residual: bond pdb=" N THR A 316 " pdb=" H1 THR A 316 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N GLU B 1 " pdb=" H1 GLU B 1 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ASP E 1 " pdb=" H2 ASP E 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLU C 1 " pdb=" H3 GLU C 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLU D 1 " pdb=" H3 GLU D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 4.72 - 30.59: 3 30.59 - 56.47: 0 56.47 - 82.35: 9 82.35 - 108.23: 3258 108.23 - 134.11: 25577 Bond angle restraints: 28847 Sorted by residual: angle pdb=" H1 GLU C 1 " pdb=" N GLU C 1 " pdb=" H3 GLU C 1 " ideal model delta sigma weight residual 109.47 4.72 104.75 3.00e+00 1.11e-01 1.22e+03 angle pdb=" H1 ASP E 1 " pdb=" N ASP E 1 " pdb=" H2 ASP E 1 " ideal model delta sigma weight residual 109.47 9.03 100.44 3.00e+00 1.11e-01 1.12e+03 angle pdb=" H1 GLU D 1 " pdb=" N GLU D 1 " pdb=" H2 GLU D 1 " ideal model delta sigma weight residual 109.47 25.92 83.55 3.00e+00 1.11e-01 7.76e+02 angle pdb=" N VAL A 428 " pdb=" CA VAL A 428 " pdb=" HA VAL A 428 " ideal model delta sigma weight residual 110.00 73.93 36.07 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C VAL A 428 " pdb=" CA VAL A 428 " pdb=" HA VAL A 428 " ideal model delta sigma weight residual 109.00 73.24 35.76 3.00e+00 1.11e-01 1.42e+02 ... (remaining 28842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 6755 17.33 - 34.65: 606 34.65 - 51.98: 171 51.98 - 69.30: 46 69.30 - 86.63: 12 Dihedral angle restraints: 7590 sinusoidal: 3936 harmonic: 3654 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 49.04 43.96 1 1.00e+01 1.00e-02 2.69e+01 dihedral pdb=" CB CYS E 134 " pdb=" SG CYS E 134 " pdb=" SG CYS E 194 " pdb=" CB CYS E 194 " ideal model delta sinusoidal sigma weight residual 93.00 50.02 42.98 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CA SER C 30 " pdb=" C SER C 30 " pdb=" N SER C 31 " pdb=" CA SER C 31 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1137 0.078 - 0.157: 106 0.157 - 0.235: 1 0.235 - 0.314: 0 0.314 - 0.392: 2 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA THR D 103 " pdb=" N THR D 103 " pdb=" C THR D 103 " pdb=" CB THR D 103 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA THR D 102 " pdb=" N THR D 102 " pdb=" C THR D 102 " pdb=" CB THR D 102 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA VAL A 428 " pdb=" N VAL A 428 " pdb=" C VAL A 428 " pdb=" CB VAL A 428 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1243 not shown) Planarity restraints: 2465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 192 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO D 193 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 167 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO B 168 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 156 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO D 157 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.016 5.00e-02 4.00e+02 ... (remaining 2462 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1038 2.19 - 2.79: 31778 2.79 - 3.40: 38663 3.40 - 4.00: 55240 4.00 - 4.60: 84984 Nonbonded interactions: 211703 Sorted by model distance: nonbonded pdb=" O SER D 52 " pdb="HH12 ARG D 72 " model vdw 1.591 1.850 nonbonded pdb="HH11 ARG A 329 " pdb=" O ALA E 91 " model vdw 1.596 1.850 nonbonded pdb=" HE ARG B 97 " pdb=" OD2 ASP B 102 " model vdw 1.622 1.850 nonbonded pdb=" H ASP E 151 " pdb=" O VAL E 191 " model vdw 1.623 1.850 nonbonded pdb="HH21 ARG D 98 " pdb=" OD2 ASP D 109 " model vdw 1.637 1.850 ... (remaining 211698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.970 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 51.510 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.520 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 0.004 0.042 8285 Z= 0.297 Angle : 0.510 4.588 11272 Z= 0.275 Chirality : 0.045 0.392 1246 Planarity : 0.003 0.034 1460 Dihedral : 15.749 86.629 2942 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.12 % Favored : 91.78 % Rotamer: Outliers : 0.90 % Allowed : 24.10 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -3.76 (0.22), residues: 1059 helix: -4.98 (0.16), residues: 54 sheet: -1.35 (0.22), residues: 450 loop : -3.32 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 155 HIS 0.002 0.001 HIS D 35 PHE 0.011 0.001 PHE B 78 TYR 0.010 0.001 TYR D 95 ARG 0.001 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 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: A 404 TYR cc_start: 0.8693 (m-10) cc_final: 0.8355 (m-10) REVERT: D 150 VAL cc_start: 0.8224 (t) cc_final: 0.8023 (t) REVERT: E 81 GLU cc_start: 0.7442 (pm20) cc_final: 0.7232 (pm20) REVERT: E 170 ASP cc_start: 0.7454 (p0) cc_final: 0.7118 (p0) REVERT: B 11 LEU cc_start: 0.8741 (tp) cc_final: 0.8337 (mt) outliers start: 8 outliers final: 4 residues processed: 156 average time/residue: 0.4335 time to fit residues: 91.0716 Evaluate side-chains 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain B residue 217 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0370 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 GLN E 124 GLN B 156 ASN C 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8285 Z= 0.192 Angle : 0.504 6.109 11272 Z= 0.266 Chirality : 0.046 0.401 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.619 39.387 1157 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 1.35 % Allowed : 23.20 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -2.81 (0.24), residues: 1059 helix: -4.47 (0.28), residues: 55 sheet: -0.74 (0.23), residues: 454 loop : -2.63 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.002 0.001 HIS D 208 PHE 0.010 0.001 PHE B 78 TYR 0.011 0.001 TYR D 95 ARG 0.002 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6715 (p90) REVERT: D 150 VAL cc_start: 0.8096 (t) cc_final: 0.7891 (t) REVERT: E 81 GLU cc_start: 0.7423 (pm20) cc_final: 0.7180 (pm20) REVERT: E 170 ASP cc_start: 0.7667 (p0) cc_final: 0.7317 (p0) REVERT: B 11 LEU cc_start: 0.8772 (tp) cc_final: 0.8378 (mt) outliers start: 12 outliers final: 6 residues processed: 121 average time/residue: 0.3978 time to fit residues: 67.0871 Evaluate side-chains 111 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 HIS B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8285 Z= 0.409 Angle : 0.579 5.248 11272 Z= 0.308 Chirality : 0.048 0.406 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.940 52.197 1153 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.20 % Favored : 89.71 % Rotamer: Outliers : 2.48 % Allowed : 22.52 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -2.39 (0.25), residues: 1059 helix: -4.29 (0.33), residues: 55 sheet: -0.44 (0.23), residues: 465 loop : -2.38 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 155 HIS 0.004 0.001 HIS D 35 PHE 0.014 0.002 PHE E 116 TYR 0.013 0.002 TYR B 94 ARG 0.002 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7564 (p90) REVERT: D 146 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7448 (pp) REVERT: E 170 ASP cc_start: 0.7908 (p0) cc_final: 0.7619 (p0) REVERT: E 190 LYS cc_start: 0.5609 (tttm) cc_final: 0.4706 (mtpp) REVERT: B 11 LEU cc_start: 0.8913 (tp) cc_final: 0.8519 (mt) REVERT: B 81 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8200 (mtmm) outliers start: 22 outliers final: 15 residues processed: 124 average time/residue: 0.4144 time to fit residues: 70.7528 Evaluate side-chains 116 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 198 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8285 Z= 0.226 Angle : 0.507 4.660 11272 Z= 0.267 Chirality : 0.046 0.396 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.636 48.134 1153 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.63 % Rotamer: Outliers : 1.91 % Allowed : 23.76 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -2.00 (0.25), residues: 1059 helix: -4.11 (0.36), residues: 55 sheet: -0.18 (0.23), residues: 465 loop : -2.12 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 155 HIS 0.003 0.001 HIS D 35 PHE 0.009 0.001 PHE E 116 TYR 0.010 0.001 TYR B 33 ARG 0.001 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7531 (p90) REVERT: D 146 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7570 (pp) REVERT: E 170 ASP cc_start: 0.7928 (p0) cc_final: 0.7612 (p0) REVERT: E 190 LYS cc_start: 0.5192 (tttm) cc_final: 0.4731 (mtpp) REVERT: B 11 LEU cc_start: 0.8846 (tp) cc_final: 0.8507 (mt) REVERT: B 81 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8171 (mtmm) outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.4245 time to fit residues: 70.7874 Evaluate side-chains 112 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 183 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN B 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8285 Z= 0.360 Angle : 0.551 5.078 11272 Z= 0.293 Chirality : 0.047 0.407 1246 Planarity : 0.004 0.032 1460 Dihedral : 4.885 51.862 1153 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.29 % Favored : 89.61 % Rotamer: Outliers : 2.82 % Allowed : 23.09 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -1.86 (0.25), residues: 1059 helix: -4.03 (0.37), residues: 55 sheet: -0.06 (0.24), residues: 459 loop : -2.02 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 155 HIS 0.005 0.001 HIS D 35 PHE 0.009 0.001 PHE E 118 TYR 0.011 0.002 TYR B 94 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7793 (p90) REVERT: D 146 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7585 (pp) REVERT: E 81 GLU cc_start: 0.7391 (pm20) cc_final: 0.7149 (pm20) REVERT: E 170 ASP cc_start: 0.8078 (p0) cc_final: 0.7800 (p0) REVERT: E 190 LYS cc_start: 0.5691 (tttm) cc_final: 0.5262 (mtpt) REVERT: B 11 LEU cc_start: 0.8883 (tp) cc_final: 0.8517 (mt) REVERT: B 81 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8234 (mtmm) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.4567 time to fit residues: 76.4831 Evaluate side-chains 123 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 183 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8285 Z= 0.223 Angle : 0.502 4.692 11272 Z= 0.265 Chirality : 0.046 0.398 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.648 48.174 1153 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 2.59 % Allowed : 23.20 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -1.63 (0.25), residues: 1059 helix: -3.80 (0.41), residues: 55 sheet: 0.07 (0.24), residues: 463 loop : -1.86 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 155 HIS 0.003 0.001 HIS D 35 PHE 0.010 0.001 PHE E 116 TYR 0.009 0.001 TYR B 33 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7618 (p90) REVERT: D 146 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7643 (pp) REVERT: E 81 GLU cc_start: 0.7380 (pm20) cc_final: 0.7134 (pm20) REVERT: E 170 ASP cc_start: 0.8041 (p0) cc_final: 0.7767 (p0) REVERT: E 190 LYS cc_start: 0.5444 (tttm) cc_final: 0.5016 (mtpt) REVERT: B 11 LEU cc_start: 0.8835 (tp) cc_final: 0.8515 (mt) REVERT: B 81 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8198 (mtmm) outliers start: 23 outliers final: 20 residues processed: 120 average time/residue: 0.4148 time to fit residues: 68.7498 Evaluate side-chains 124 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 183 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8285 Z= 0.341 Angle : 0.538 4.958 11272 Z= 0.285 Chirality : 0.047 0.407 1246 Planarity : 0.004 0.034 1460 Dihedral : 4.823 50.852 1153 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.92 % Favored : 89.99 % Rotamer: Outliers : 3.15 % Allowed : 22.75 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -1.54 (0.26), residues: 1059 helix: -3.65 (0.45), residues: 55 sheet: 0.10 (0.24), residues: 464 loop : -1.79 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 32 HIS 0.005 0.001 HIS D 35 PHE 0.010 0.001 PHE E 116 TYR 0.011 0.002 TYR B 94 ARG 0.002 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7812 (p90) REVERT: D 146 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7659 (pp) REVERT: E 81 GLU cc_start: 0.7428 (pm20) cc_final: 0.7176 (pm20) REVERT: E 170 ASP cc_start: 0.8153 (p0) cc_final: 0.7865 (p0) REVERT: E 190 LYS cc_start: 0.5601 (tttm) cc_final: 0.5179 (mtpt) REVERT: B 11 LEU cc_start: 0.8870 (tp) cc_final: 0.8516 (mt) REVERT: B 81 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8234 (mtmm) outliers start: 28 outliers final: 23 residues processed: 128 average time/residue: 0.4549 time to fit residues: 79.1710 Evaluate side-chains 131 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 186 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 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 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8285 Z= 0.183 Angle : 0.488 4.550 11272 Z= 0.257 Chirality : 0.046 0.400 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.513 45.356 1153 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 2.82 % Allowed : 22.86 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -1.29 (0.26), residues: 1059 helix: -3.43 (0.48), residues: 55 sheet: 0.23 (0.24), residues: 464 loop : -1.58 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.002 0.001 HIS D 35 PHE 0.009 0.001 PHE E 116 TYR 0.009 0.001 TYR B 33 ARG 0.002 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7565 (p90) REVERT: E 81 GLU cc_start: 0.7419 (pm20) cc_final: 0.7182 (pm20) REVERT: E 170 ASP cc_start: 0.8101 (p0) cc_final: 0.7804 (p0) REVERT: E 190 LYS cc_start: 0.5391 (tttm) cc_final: 0.4959 (mtpt) REVERT: B 11 LEU cc_start: 0.8825 (tp) cc_final: 0.8518 (mt) REVERT: B 81 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8208 (mtmm) REVERT: C 82 GLU cc_start: 0.7768 (mp0) cc_final: 0.7495 (pm20) outliers start: 25 outliers final: 22 residues processed: 124 average time/residue: 0.4252 time to fit residues: 72.2766 Evaluate side-chains 127 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 183 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 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 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8285 Z= 0.183 Angle : 0.484 4.470 11272 Z= 0.254 Chirality : 0.046 0.400 1246 Planarity : 0.004 0.034 1460 Dihedral : 4.315 40.775 1153 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 2.14 % Allowed : 23.42 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -1.05 (0.26), residues: 1059 helix: -3.17 (0.52), residues: 55 sheet: 0.37 (0.24), residues: 463 loop : -1.40 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 155 HIS 0.003 0.001 HIS D 208 PHE 0.009 0.001 PHE E 116 TYR 0.014 0.001 TYR C 141 ARG 0.002 0.000 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7454 (p90) REVERT: E 81 GLU cc_start: 0.7349 (pm20) cc_final: 0.7109 (pm20) REVERT: E 170 ASP cc_start: 0.8135 (p0) cc_final: 0.7833 (p0) REVERT: E 190 LYS cc_start: 0.5258 (tttm) cc_final: 0.4836 (mtpt) REVERT: B 11 LEU cc_start: 0.8841 (tp) cc_final: 0.8520 (mt) REVERT: B 81 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: C 82 GLU cc_start: 0.7776 (mp0) cc_final: 0.7527 (pm20) outliers start: 19 outliers final: 17 residues processed: 118 average time/residue: 0.3960 time to fit residues: 65.9450 Evaluate side-chains 123 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8285 Z= 0.216 Angle : 0.500 7.892 11272 Z= 0.263 Chirality : 0.046 0.404 1246 Planarity : 0.004 0.035 1460 Dihedral : 4.382 40.534 1153 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 2.48 % Allowed : 23.09 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -0.97 (0.26), residues: 1059 helix: -3.02 (0.53), residues: 55 sheet: 0.39 (0.24), residues: 461 loop : -1.33 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS D 208 PHE 0.009 0.001 PHE B 78 TYR 0.013 0.001 TYR C 141 ARG 0.002 0.000 ARG C 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 316 is missing expected H atoms. Skipping. Residue SER 382 is missing expected H atoms. Skipping. Residue SER 187 is missing expected H atoms. Skipping. Residue THR 5 is missing expected H atoms. Skipping. Residue SER 131 is missing expected H atoms. Skipping. Residue VAL 132 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 191 is missing expected H atoms. Skipping. Residue LEU 18 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LEU 45 is missing expected H atoms. Skipping. Residue THR 108 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue SER 154 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue ILE 118 is missing expected H atoms. Skipping. Residue SER 160 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue VAL 192 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7494 (p90) REVERT: E 81 GLU cc_start: 0.7342 (pm20) cc_final: 0.7117 (pm20) REVERT: E 170 ASP cc_start: 0.8145 (p0) cc_final: 0.7835 (p0) REVERT: E 190 LYS cc_start: 0.5307 (tttm) cc_final: 0.4904 (mtpt) REVERT: B 11 LEU cc_start: 0.8841 (tp) cc_final: 0.8523 (mt) REVERT: B 81 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8211 (mtmm) REVERT: C 82 GLU cc_start: 0.7861 (mp0) cc_final: 0.7557 (pm20) outliers start: 22 outliers final: 19 residues processed: 121 average time/residue: 0.4211 time to fit residues: 72.2624 Evaluate side-chains 123 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 209 PHE Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 183 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 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 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.134463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099421 restraints weight = 30489.829| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.02 r_work: 0.2903 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8285 Z= 0.216 Angle : 0.497 7.611 11272 Z= 0.262 Chirality : 0.046 0.403 1246 Planarity : 0.004 0.035 1460 Dihedral : 4.353 40.398 1153 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.63 % Rotamer: Outliers : 2.48 % Allowed : 23.20 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % 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: -0.89 (0.26), residues: 1059 helix: -2.87 (0.56), residues: 55 sheet: 0.42 (0.24), residues: 461 loop : -1.25 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS D 35 PHE 0.009 0.001 PHE B 78 TYR 0.011 0.001 TYR C 141 ARG 0.002 0.000 ARG C 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.04 seconds wall clock time: 72 minutes 31.69 seconds (4351.69 seconds total)