Starting phenix.real_space_refine on Thu Nov 16 15:27:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/11_2023/7xcz_33130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/11_2023/7xcz_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_33130/11_2023/7xcz_33130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/11_2023/7xcz_33130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/11_2023/7xcz_33130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/11_2023/7xcz_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-1.21rc1-5144/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: 7.15, 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: 12.33 Conformation dependent library (CDL) restraints added in 1.7 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: 1.33 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: 5.71 Time building geometry restraints manager: 12.69 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: 5784 17.33 - 34.65: 556 34.65 - 51.98: 130 51.98 - 69.30: 44 69.30 - 86.63: 12 Dihedral angle restraints: 6526 sinusoidal: 2872 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 6523 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: 2.250 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: 0.220 Extract box with map and model: 10.610 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 50.340 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.870 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.238 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 outliers start: 8 outliers final: 4 residues processed: 156 average time/residue: 0.4584 time to fit residues: 96.6942 Evaluate side-chains 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1678 time to fit residues: 2.7844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 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: 0.7980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 E 198 HIS B 156 ASN C 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8285 Z= 0.266 Angle : 0.538 6.915 11272 Z= 0.284 Chirality : 0.047 0.404 1246 Planarity : 0.004 0.032 1460 Dihedral : 4.577 44.985 1153 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.74 % Favored : 92.16 % Rotamer: Outliers : 1.80 % Allowed : 22.30 % Favored : 75.90 % 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: -2.80 (0.24), residues: 1059 helix: -4.50 (0.30), residues: 55 sheet: -0.70 (0.23), residues: 455 loop : -2.66 (0.24), residues: 549 *********************** 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 127 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 125 average time/residue: 0.4490 time to fit residues: 75.6726 Evaluate side-chains 111 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1719 time to fit residues: 4.4180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 1.9990 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: 2.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 199 GLN B 6 GLN B 56 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8285 Z= 0.406 Angle : 0.587 5.166 11272 Z= 0.311 Chirality : 0.049 0.405 1246 Planarity : 0.004 0.031 1460 Dihedral : 5.016 52.596 1153 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.29 % Favored : 89.61 % Rotamer: Outliers : 1.46 % Allowed : 22.75 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.95 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.28 (0.34), residues: 55 sheet: -0.42 (0.23), residues: 465 loop : -2.42 (0.25), residues: 539 *********************** 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 113 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 112 average time/residue: 0.4244 time to fit residues: 65.4557 Evaluate side-chains 105 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1701 time to fit residues: 3.5786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8285 Z= 0.233 Angle : 0.518 4.726 11272 Z= 0.272 Chirality : 0.046 0.400 1246 Planarity : 0.003 0.029 1460 Dihedral : 4.716 48.814 1153 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 0.79 % Allowed : 23.42 % Favored : 75.79 % 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: -2.05 (0.25), residues: 1059 helix: -4.13 (0.36), residues: 55 sheet: -0.18 (0.24), residues: 459 loop : -2.17 (0.26), residues: 545 *********************** 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 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 111 average time/residue: 0.4077 time to fit residues: 63.2301 Evaluate side-chains 110 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1928 time to fit residues: 3.5607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- 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 B 50 GLN B 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8285 Z= 0.192 Angle : 0.495 4.616 11272 Z= 0.259 Chirality : 0.046 0.402 1246 Planarity : 0.003 0.030 1460 Dihedral : 4.464 44.389 1153 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 0.79 % Allowed : 23.09 % Favored : 76.13 % 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: -1.72 (0.25), residues: 1059 helix: -3.93 (0.38), residues: 55 sheet: 0.01 (0.24), residues: 462 loop : -1.91 (0.26), residues: 542 *********************** 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 111 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 109 average time/residue: 0.4086 time to fit residues: 61.9904 Evaluate side-chains 104 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1766 time to fit residues: 2.7979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8285 Z= 0.307 Angle : 0.531 4.916 11272 Z= 0.280 Chirality : 0.047 0.405 1246 Planarity : 0.003 0.032 1460 Dihedral : 4.674 47.801 1153 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.25 % Favored : 90.65 % Rotamer: Outliers : 0.68 % Allowed : 22.97 % Favored : 76.35 % 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: -1.59 (0.25), residues: 1059 helix: -3.83 (0.40), residues: 55 sheet: 0.09 (0.24), residues: 464 loop : -1.83 (0.26), residues: 540 *********************** 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 108 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 106 average time/residue: 0.4326 time to fit residues: 63.9503 Evaluate side-chains 104 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1713 time to fit residues: 2.8300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 62 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 A 470 ASN C 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8285 Z= 0.179 Angle : 0.491 4.514 11272 Z= 0.258 Chirality : 0.046 0.400 1246 Planarity : 0.003 0.031 1460 Dihedral : 4.431 43.629 1153 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.67 % Rotamer: Outliers : 0.56 % Allowed : 23.09 % Favored : 76.35 % 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: -1.33 (0.26), residues: 1059 helix: -3.48 (0.45), residues: 55 sheet: 0.22 (0.24), residues: 462 loop : -1.61 (0.27), residues: 542 *********************** 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 109 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 107 average time/residue: 0.4070 time to fit residues: 60.9810 Evaluate side-chains 105 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1932 time to fit residues: 2.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8285 Z= 0.199 Angle : 0.499 5.829 11272 Z= 0.262 Chirality : 0.046 0.405 1246 Planarity : 0.003 0.032 1460 Dihedral : 4.348 41.217 1153 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.74 % Favored : 92.16 % Rotamer: Outliers : 0.34 % Allowed : 23.09 % Favored : 76.58 % 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: -1.14 (0.26), residues: 1059 helix: -3.24 (0.50), residues: 55 sheet: 0.33 (0.24), residues: 463 loop : -1.49 (0.27), residues: 541 *********************** 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 105 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 103 average time/residue: 0.4220 time to fit residues: 61.8015 Evaluate side-chains 101 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2060 time to fit residues: 2.6370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8285 Z= 0.202 Angle : 0.497 5.011 11272 Z= 0.262 Chirality : 0.046 0.404 1246 Planarity : 0.003 0.032 1460 Dihedral : 4.317 40.079 1153 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 0.11 % Allowed : 23.42 % Favored : 76.46 % 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: -0.99 (0.26), residues: 1059 helix: -3.07 (0.53), residues: 55 sheet: 0.41 (0.24), residues: 463 loop : -1.38 (0.27), residues: 541 *********************** 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 107 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 106 average time/residue: 0.4113 time to fit residues: 61.1467 Evaluate side-chains 103 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1652 time to fit residues: 1.8444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.0670 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8285 Z= 0.168 Angle : 0.487 6.280 11272 Z= 0.256 Chirality : 0.046 0.405 1246 Planarity : 0.003 0.032 1460 Dihedral : 4.213 38.921 1153 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 0.11 % Allowed : 23.76 % Favored : 76.13 % 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: -0.84 (0.26), residues: 1059 helix: -2.89 (0.55), residues: 55 sheet: 0.48 (0.25), residues: 461 loop : -1.24 (0.27), residues: 543 ********************** 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 105 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 104 average time/residue: 0.4026 time to fit residues: 59.9954 Evaluate side-chains 99 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2273 time to fit residues: 1.9789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 76 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.135256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100124 restraints weight = 30411.837| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.12 r_work: 0.2893 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8285 Z= 0.201 Angle : 0.498 6.092 11272 Z= 0.261 Chirality : 0.046 0.405 1246 Planarity : 0.003 0.033 1460 Dihedral : 4.252 40.522 1153 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 24.21 % Favored : 75.79 % 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: -0.77 (0.26), residues: 1059 helix: -2.79 (0.57), residues: 55 sheet: 0.52 (0.25), residues: 463 loop : -1.20 (0.27), residues: 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3917.61 seconds wall clock time: 70 minutes 14.98 seconds (4214.98 seconds total)