Starting phenix.real_space_refine on Fri Feb 16 16:05:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/02_2024/7xcz_33130.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/02_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_33130/02_2024/7xcz_33130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/02_2024/7xcz_33130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/02_2024/7xcz_33130.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xcz_33130/02_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-dev-5238/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: 7.50, per 1000 atoms: 0.47 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: 12.70 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: 1.42 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: 5.90 Time building geometry restraints manager: 13.08 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: 6804 17.33 - 34.65: 666 34.65 - 51.98: 210 51.98 - 69.30: 64 69.30 - 86.63: 12 Dihedral angle restraints: 7756 sinusoidal: 4102 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 7753 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: 3.290 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: 0.230 Extract box with map and model: 10.720 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 52.930 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.690 ------------------------------------------------------------------------------- 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 : 1.356 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: 0.4395 time to fit residues: 92.5095 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: 0.8980 chunk 79 optimal weight: 0.8980 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: 1.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8285 Z= 0.256 Angle : 0.531 5.132 11272 Z= 0.281 Chirality : 0.047 0.404 1246 Planarity : 0.004 0.035 1460 Dihedral : 4.825 44.317 1157 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.65 % Favored : 92.26 % Rotamer: Outliers : 1.80 % Allowed : 22.86 % Favored : 75.34 % 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: -2.79 (0.24), residues: 1059 helix: -4.49 (0.29), residues: 55 sheet: -0.71 (0.23), residues: 455 loop : -2.63 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 155 HIS 0.002 0.001 HIS D 208 PHE 0.010 0.001 PHE C 99 TYR 0.012 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 127 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.267 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: 0.8007 (OUTLIER) cc_final: 0.6989 (p90) REVERT: D 150 VAL cc_start: 0.8118 (t) cc_final: 0.7914 (t) REVERT: E 170 ASP cc_start: 0.7788 (p0) cc_final: 0.7418 (p0) REVERT: E 190 LYS cc_start: 0.5244 (tttm) cc_final: 0.4792 (mtpp) REVERT: B 11 LEU cc_start: 0.8902 (tp) cc_final: 0.8494 (mt) outliers start: 16 outliers final: 9 residues processed: 126 average time/residue: 0.4435 time to fit residues: 75.7075 Evaluate side-chains 113 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 PHE 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 205 ASN Chi-restraints excluded: chain E residue 30 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8285 Z= 0.220 Angle : 0.497 4.607 11272 Z= 0.261 Chirality : 0.046 0.400 1246 Planarity : 0.003 0.031 1460 Dihedral : 4.442 42.960 1153 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.48 % Rotamer: Outliers : 1.69 % Allowed : 23.65 % Favored : 74.66 % 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: -2.26 (0.25), residues: 1059 helix: -4.24 (0.32), residues: 55 sheet: -0.42 (0.23), residues: 458 loop : -2.20 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.003 0.001 HIS C 190 PHE 0.013 0.001 PHE E 116 TYR 0.011 0.001 TYR A 352 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 118 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7172 (p90) REVERT: D 146 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7440 (pp) REVERT: E 81 GLU cc_start: 0.7443 (pm20) cc_final: 0.7197 (pm20) REVERT: E 170 ASP cc_start: 0.7852 (p0) cc_final: 0.7524 (p0) REVERT: E 190 LYS cc_start: 0.5279 (tttm) cc_final: 0.4349 (mtpp) REVERT: B 11 LEU cc_start: 0.8831 (tp) cc_final: 0.8454 (mt) REVERT: B 81 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8170 (mtmm) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.4187 time to fit residues: 66.9412 Evaluate side-chains 112 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 30 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8285 Z= 0.206 Angle : 0.490 4.647 11272 Z= 0.257 Chirality : 0.046 0.400 1246 Planarity : 0.003 0.031 1460 Dihedral : 4.336 40.918 1153 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 1.69 % Allowed : 23.31 % 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: -1.84 (0.25), residues: 1059 helix: -3.98 (0.37), residues: 55 sheet: -0.08 (0.24), residues: 452 loop : -1.96 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 155 HIS 0.002 0.001 HIS C 190 PHE 0.011 0.001 PHE E 116 TYR 0.008 0.001 TYR E 86 ARG 0.001 0.000 ARG C 18 *********************** 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 118 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.460 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: 0.8321 (OUTLIER) cc_final: 0.7275 (p90) REVERT: D 146 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7550 (pp) REVERT: D 179 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7074 (mp10) REVERT: E 170 ASP cc_start: 0.7888 (p0) cc_final: 0.7557 (p0) REVERT: E 190 LYS cc_start: 0.5144 (tttm) cc_final: 0.4702 (mtpp) REVERT: B 11 LEU cc_start: 0.8820 (tp) cc_final: 0.8464 (mt) REVERT: B 81 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8146 (mtmm) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 0.4330 time to fit residues: 69.6814 Evaluate side-chains 112 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 96 CYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 56 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2688 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 : 0.491 4.700 11272 Z= 0.258 Chirality : 0.046 0.400 1246 Planarity : 0.004 0.031 1460 Dihedral : 4.363 41.185 1153 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.55 % Favored : 92.35 % Rotamer: Outliers : 2.14 % Allowed : 22.86 % 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: -1.57 (0.26), residues: 1059 helix: -3.90 (0.39), residues: 55 sheet: 0.08 (0.24), residues: 461 loop : -1.77 (0.26), residues: 543 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 0.011 0.001 PHE E 116 TYR 0.009 0.001 TYR E 86 ARG 0.001 0.000 ARG E 211 *********************** 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 120 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.405 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: 0.8388 (OUTLIER) cc_final: 0.7431 (p90) REVERT: D 146 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7605 (pp) REVERT: D 179 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: E 81 GLU cc_start: 0.7416 (pm20) cc_final: 0.7180 (pm20) REVERT: E 170 ASP cc_start: 0.7986 (p0) cc_final: 0.7669 (p0) REVERT: E 190 LYS cc_start: 0.5260 (tttm) cc_final: 0.4853 (mtpt) REVERT: B 11 LEU cc_start: 0.8821 (tp) cc_final: 0.8467 (mt) REVERT: B 81 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8171 (mtmm) outliers start: 19 outliers final: 15 residues processed: 118 average time/residue: 0.4276 time to fit residues: 70.2439 Evaluate side-chains 121 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain D residue 205 ASN 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 183 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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** C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8285 Z= 0.189 Angle : 0.477 4.577 11272 Z= 0.250 Chirality : 0.046 0.400 1246 Planarity : 0.004 0.032 1460 Dihedral : 4.252 39.307 1153 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.48 % Rotamer: Outliers : 2.14 % Allowed : 23.20 % Favored : 74.66 % 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: -1.34 (0.26), residues: 1059 helix: -3.67 (0.42), residues: 55 sheet: 0.19 (0.24), residues: 460 loop : -1.56 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS D 35 PHE 0.009 0.001 PHE B 78 TYR 0.008 0.001 TYR E 86 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 123 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.197 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: 0.8343 (OUTLIER) cc_final: 0.7326 (p90) REVERT: D 146 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7630 (pp) REVERT: D 179 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: E 81 GLU cc_start: 0.7389 (pm20) cc_final: 0.7142 (pm20) REVERT: E 170 ASP cc_start: 0.7999 (p0) cc_final: 0.7702 (p0) REVERT: E 190 LYS cc_start: 0.5233 (tttm) cc_final: 0.4841 (mtpt) REVERT: B 11 LEU cc_start: 0.8872 (tp) cc_final: 0.8511 (mt) REVERT: B 81 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8173 (mtmm) REVERT: C 82 GLU cc_start: 0.7653 (mp0) cc_final: 0.7364 (pm20) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.3968 time to fit residues: 65.9664 Evaluate side-chains 118 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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 179 GLN Chi-restraints excluded: chain D residue 205 ASN Chi-restraints excluded: chain E residue 11 VAL 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 C residue 64 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.2961 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= 0.214 Angle : 0.484 4.655 11272 Z= 0.254 Chirality : 0.046 0.401 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.292 40.158 1153 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.65 % Favored : 92.26 % Rotamer: Outliers : 2.36 % Allowed : 22.18 % 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: -1.16 (0.26), residues: 1059 helix: -3.52 (0.45), residues: 55 sheet: 0.27 (0.24), residues: 466 loop : -1.42 (0.27), residues: 538 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 0.010 0.001 PHE E 116 TYR 0.008 0.001 TYR B 94 ARG 0.001 0.000 ARG C 55 *********************** 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 124 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 1.546 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: 0.8375 (OUTLIER) cc_final: 0.7310 (p90) REVERT: E 170 ASP cc_start: 0.8080 (p0) cc_final: 0.7792 (p0) REVERT: E 190 LYS cc_start: 0.5252 (tttm) cc_final: 0.4856 (mtpt) REVERT: B 11 LEU cc_start: 0.8816 (tp) cc_final: 0.8468 (mt) REVERT: B 81 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8191 (mtmm) REVERT: C 82 GLU cc_start: 0.7652 (mp0) cc_final: 0.7445 (pm20) outliers start: 21 outliers final: 17 residues processed: 122 average time/residue: 0.4058 time to fit residues: 69.0983 Evaluate side-chains 119 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 132 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 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 183 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 D 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8285 Z= 0.194 Angle : 0.478 4.581 11272 Z= 0.250 Chirality : 0.046 0.401 1246 Planarity : 0.003 0.033 1460 Dihedral : 4.229 39.412 1153 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.23 % Favored : 93.67 % Rotamer: Outliers : 2.36 % Allowed : 22.07 % Favored : 75.56 % 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: -1.00 (0.26), residues: 1059 helix: -3.29 (0.49), residues: 55 sheet: 0.45 (0.25), residues: 455 loop : -1.37 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 32 HIS 0.002 0.001 HIS D 35 PHE 0.010 0.001 PHE E 116 TYR 0.008 0.001 TYR E 86 ARG 0.001 0.000 ARG C 55 *********************** 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 125 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 1.298 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: 0.8368 (OUTLIER) cc_final: 0.7418 (p90) REVERT: D 16 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7531 (mtp85) REVERT: E 170 ASP cc_start: 0.8084 (p0) cc_final: 0.7788 (p0) REVERT: E 190 LYS cc_start: 0.5209 (tttm) cc_final: 0.4822 (mtpt) REVERT: B 11 LEU cc_start: 0.8807 (tp) cc_final: 0.8454 (mt) REVERT: B 81 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8184 (mtmm) REVERT: C 82 GLU cc_start: 0.7657 (mp0) cc_final: 0.7444 (pm20) outliers start: 21 outliers final: 17 residues processed: 122 average time/residue: 0.4076 time to fit residues: 68.7950 Evaluate side-chains 114 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 105 ASP Chi-restraints excluded: chain D residue 132 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 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 C residue 64 SER 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: 0.7980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN C 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8285 Z= 0.159 Angle : 0.466 4.432 11272 Z= 0.244 Chirality : 0.046 0.402 1246 Planarity : 0.003 0.032 1460 Dihedral : 4.119 38.735 1153 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 1.91 % Allowed : 22.07 % Favored : 76.01 % 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: -0.83 (0.26), residues: 1059 helix: -3.10 (0.52), residues: 55 sheet: 0.54 (0.25), residues: 455 loop : -1.25 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.002 0.001 HIS D 208 PHE 0.008 0.001 PHE B 78 TYR 0.007 0.001 TYR E 86 ARG 0.003 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 113 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.152 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: 0.8285 (OUTLIER) cc_final: 0.7135 (p90) REVERT: E 170 ASP cc_start: 0.8080 (p0) cc_final: 0.7766 (p0) REVERT: E 190 LYS cc_start: 0.5052 (tttm) cc_final: 0.4651 (mtpt) REVERT: B 11 LEU cc_start: 0.8803 (tp) cc_final: 0.8453 (mt) REVERT: B 81 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8163 (mtmm) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.3968 time to fit residues: 60.8313 Evaluate side-chains 115 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 33 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 121 SER Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 96 optimal weight: 0.2980 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8049 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8285 Z= 0.164 Angle : 0.468 4.404 11272 Z= 0.244 Chirality : 0.046 0.402 1246 Planarity : 0.004 0.033 1460 Dihedral : 4.090 38.874 1153 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 1.91 % Allowed : 22.30 % 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: -0.71 (0.26), residues: 1059 helix: -2.92 (0.55), residues: 55 sheet: 0.61 (0.25), residues: 455 loop : -1.15 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 47 HIS 0.003 0.001 HIS D 208 PHE 0.008 0.001 PHE B 78 TYR 0.016 0.001 TYR C 141 ARG 0.004 0.000 ARG D 16 ********************** 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 119 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.274 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: 0.8267 (OUTLIER) cc_final: 0.7109 (p90) REVERT: E 170 ASP cc_start: 0.8088 (p0) cc_final: 0.7757 (p0) REVERT: E 190 LYS cc_start: 0.4895 (tttm) cc_final: 0.4509 (mtpt) REVERT: B 11 LEU cc_start: 0.8803 (tp) cc_final: 0.8452 (mt) REVERT: B 81 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: C 82 GLU cc_start: 0.7659 (mp0) cc_final: 0.7443 (pm20) outliers start: 17 outliers final: 14 residues processed: 116 average time/residue: 0.3926 time to fit residues: 64.2256 Evaluate side-chains 116 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 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 33 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 C residue 64 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: 0.0040 chunk 25 optimal weight: 0.0270 chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 73 optimal weight: 0.9990 overall best weight: 0.2088 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.138928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104633 restraints weight = 30268.989| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.92 r_work: 0.2943 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8285 Z= 0.131 Angle : 0.466 7.196 11272 Z= 0.243 Chirality : 0.046 0.401 1246 Planarity : 0.004 0.034 1460 Dihedral : 3.938 33.349 1153 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.90 % Rotamer: Outliers : 1.35 % Allowed : 22.75 % 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: -0.53 (0.26), residues: 1059 helix: -2.77 (0.57), residues: 55 sheet: 0.68 (0.25), residues: 452 loop : -0.97 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 7 HIS 0.003 0.001 HIS D 208 PHE 0.008 0.001 PHE B 78 TYR 0.012 0.001 TYR C 141 ARG 0.004 0.000 ARG D 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4072.16 seconds wall clock time: 72 minutes 45.48 seconds (4365.48 seconds total)