Starting phenix.real_space_refine on Fri Mar 15 04:47:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5k_10700/03_2024/6y5k_10700.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5k_10700/03_2024/6y5k_10700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5k_10700/03_2024/6y5k_10700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5k_10700/03_2024/6y5k_10700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5k_10700/03_2024/6y5k_10700.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5k_10700/03_2024/6y5k_10700.pdb" } resolution = 4.2 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= 0.003 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6609 2.51 5 N 1854 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ASP 63": "OD1" <-> "OD2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10614 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 292} Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 292} Chain: "E" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2414 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 292} Chain: "D" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain: "F" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1096 Classifications: {'peptide': 133} Link IDs: {'TRANS': 132} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.29, per 1000 atoms: 0.59 Number of scatterers: 10614 At special positions: 0 Unit cell: (101.091, 98.917, 159.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2097 8.00 N 1854 7.00 C 6609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=1.75 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.46 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.00 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.79 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.46 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.00 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.04 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=1.78 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.46 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.00 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.04 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 38 " " NAG C 401 " - " ASN C 38 " " NAG E 401 " - " ASN E 38 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.9 seconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 36 sheets defined 32.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.117A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.699A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 126 Processing helix chain 'B' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.116A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.699A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.116A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.700A pdb=" N GLN E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 126 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 Processing helix chain 'F' and resid 38 through 126 Processing helix chain 'F' and resid 145 through 154 removed outlier: 3.800A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.964A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 120 through 122 removed outlier: 6.703A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.965A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 122 removed outlier: 6.703A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.495A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 153 Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.619A pdb=" N THR E 24 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 51 through 52 removed outlier: 5.964A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 58 through 61 removed outlier: 6.519A pdb=" N LEU E 59 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 120 through 122 removed outlier: 6.702A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD4, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.494A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.924A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 151 through 153 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD7, first strand: chain 'E' and resid 286 through 288 removed outlier: 4.184A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'F' and resid 130 through 132 483 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3567 1.34 - 1.46: 2442 1.46 - 1.59: 4743 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 10824 Sorted by residual: bond pdb=" N CYS A 305 " pdb=" CA CYS A 305 " ideal model delta sigma weight residual 1.455 1.492 -0.036 1.17e-02 7.31e+03 9.71e+00 bond pdb=" N CYS C 305 " pdb=" CA CYS C 305 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.17e-02 7.31e+03 9.44e+00 bond pdb=" N CYS E 305 " pdb=" CA CYS E 305 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.17e-02 7.31e+03 9.32e+00 bond pdb=" N LYS C 50 " pdb=" CA LYS C 50 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.22e+00 bond pdb=" N LYS E 50 " pdb=" CA LYS E 50 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.23e-02 6.61e+03 7.15e+00 ... (remaining 10819 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.41: 291 106.41 - 113.36: 6005 113.36 - 120.31: 3783 120.31 - 127.26: 4486 127.26 - 134.21: 120 Bond angle restraints: 14685 Sorted by residual: angle pdb=" C CYS C 305 " pdb=" CA CYS C 305 " pdb=" CB CYS C 305 " ideal model delta sigma weight residual 110.47 104.21 6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" C CYS A 305 " pdb=" CA CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sigma weight residual 110.47 104.21 6.26 1.77e+00 3.19e-01 1.25e+01 angle pdb=" C CYS E 305 " pdb=" CA CYS E 305 " pdb=" CB CYS E 305 " ideal model delta sigma weight residual 110.47 104.22 6.25 1.77e+00 3.19e-01 1.25e+01 angle pdb=" O CYS C 76 " pdb=" C CYS C 76 " pdb=" N ASP C 77 " ideal model delta sigma weight residual 121.99 125.98 -3.99 1.24e+00 6.50e-01 1.03e+01 angle pdb=" O CYS E 76 " pdb=" C CYS E 76 " pdb=" N ASP E 77 " ideal model delta sigma weight residual 121.99 125.97 -3.98 1.24e+00 6.50e-01 1.03e+01 ... (remaining 14680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 6035 17.15 - 34.31: 446 34.31 - 51.46: 145 51.46 - 68.61: 16 68.61 - 85.76: 12 Dihedral angle restraints: 6654 sinusoidal: 2790 harmonic: 3864 Sorted by residual: dihedral pdb=" CB CYS E 14 " pdb=" SG CYS E 14 " pdb=" SG CYS F 137 " pdb=" CB CYS F 137 " ideal model delta sinusoidal sigma weight residual -86.00 -159.46 73.46 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS D 137 " pdb=" CB CYS D 137 " ideal model delta sinusoidal sigma weight residual -86.00 -158.92 72.92 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS A 14 " pdb=" SG CYS A 14 " pdb=" SG CYS B 137 " pdb=" CB CYS B 137 " ideal model delta sinusoidal sigma weight residual -86.00 -158.43 72.43 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 6651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1252 0.050 - 0.100: 291 0.100 - 0.150: 80 0.150 - 0.200: 23 0.200 - 0.250: 4 Chirality restraints: 1650 Sorted by residual: chirality pdb=" CA CYS A 305 " pdb=" N CYS A 305 " pdb=" C CYS A 305 " pdb=" CB CYS A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA CYS E 305 " pdb=" N CYS E 305 " pdb=" C CYS E 305 " pdb=" CB CYS E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA CYS C 305 " pdb=" N CYS C 305 " pdb=" C CYS C 305 " pdb=" CB CYS C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1647 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 190 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C GLU A 190 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN A 191 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 190 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C GLU E 190 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU E 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN E 191 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 190 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.46e+00 pdb=" C GLU C 190 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU C 190 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 191 " 0.016 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 197 2.66 - 3.22: 9844 3.22 - 3.78: 16679 3.78 - 4.34: 22090 4.34 - 4.90: 35982 Nonbonded interactions: 84792 Sorted by model distance: nonbonded pdb=" OG1 THR C 24 " pdb=" O VAL C 36 " model vdw 2.096 2.440 nonbonded pdb=" OG1 THR A 24 " pdb=" O VAL A 36 " model vdw 2.097 2.440 nonbonded pdb=" OG1 THR E 24 " pdb=" O VAL E 36 " model vdw 2.097 2.440 nonbonded pdb=" NH1 ARG D 76 " pdb=" OE2 GLU F 74 " model vdw 2.190 2.520 nonbonded pdb=" OD1 ASP C 275 " pdb=" N THR C 276 " model vdw 2.196 2.520 ... (remaining 84787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.470 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.340 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 0.036 10824 Z= 0.257 Angle : 0.758 10.288 14685 Z= 0.435 Chirality : 0.051 0.250 1650 Planarity : 0.004 0.043 1917 Dihedral : 13.059 85.764 4110 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.98 (0.20), residues: 1323 helix: 0.39 (0.23), residues: 408 sheet: -0.52 (0.31), residues: 267 loop : -2.93 (0.17), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 222 HIS 0.002 0.001 HIS E 184 PHE 0.007 0.001 PHE A 79 TYR 0.012 0.002 TYR C 178 ARG 0.002 0.000 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.8238 (m-80) cc_final: 0.7727 (m-80) REVERT: B 58 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9094 (mttm) REVERT: B 64 HIS cc_start: 0.8925 (m-70) cc_final: 0.8573 (m-70) REVERT: B 65 GLN cc_start: 0.9440 (mm-40) cc_final: 0.8796 (tp-100) REVERT: B 66 ILE cc_start: 0.9717 (mt) cc_final: 0.9499 (mt) REVERT: B 69 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8491 (mt-10) REVERT: B 86 ASP cc_start: 0.8260 (t0) cc_final: 0.7850 (t0) REVERT: C 98 TYR cc_start: 0.8956 (t80) cc_final: 0.8240 (t80) REVERT: C 137 ASN cc_start: 0.9480 (m-40) cc_final: 0.9038 (p0) REVERT: E 50 LYS cc_start: 0.8581 (mttt) cc_final: 0.8120 (tptm) REVERT: E 87 PHE cc_start: 0.7100 (t80) cc_final: 0.6662 (t80) REVERT: E 98 TYR cc_start: 0.8297 (t80) cc_final: 0.7881 (t80) REVERT: E 233 TYR cc_start: 0.7983 (m-80) cc_final: 0.7715 (m-80) REVERT: D 39 LYS cc_start: 0.9733 (mptt) cc_final: 0.9515 (mmtm) REVERT: D 58 LYS cc_start: 0.9461 (mtmt) cc_final: 0.9051 (mttm) REVERT: D 62 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8598 (mmtt) REVERT: D 64 HIS cc_start: 0.8922 (m-70) cc_final: 0.8518 (m90) REVERT: D 86 ASP cc_start: 0.8450 (t0) cc_final: 0.8011 (t0) REVERT: D 108 ILE cc_start: 0.9723 (mt) cc_final: 0.9434 (tt) REVERT: F 38 LEU cc_start: 0.9521 (pt) cc_final: 0.9318 (pt) REVERT: F 39 LYS cc_start: 0.9736 (mptt) cc_final: 0.9515 (mmtm) REVERT: F 55 VAL cc_start: 0.9734 (m) cc_final: 0.9441 (m) REVERT: F 58 LYS cc_start: 0.9404 (mtmt) cc_final: 0.9135 (mttm) REVERT: F 59 THR cc_start: 0.9595 (p) cc_final: 0.8865 (p) REVERT: F 63 PHE cc_start: 0.9340 (m-10) cc_final: 0.9002 (m-80) REVERT: F 64 HIS cc_start: 0.8930 (m-70) cc_final: 0.8520 (m90) REVERT: F 65 GLN cc_start: 0.9404 (mm-40) cc_final: 0.8907 (tp-100) REVERT: F 66 ILE cc_start: 0.9704 (mt) cc_final: 0.9377 (mt) REVERT: F 69 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8398 (mm-30) REVERT: F 70 PHE cc_start: 0.8781 (m-80) cc_final: 0.8220 (m-80) REVERT: F 78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8497 (mm-40) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3098 time to fit residues: 110.2157 Evaluate side-chains 149 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 184 HIS A 216 ASN A 285 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS C 173 ASN C 184 HIS C 216 ASN C 285 ASN E 173 ASN E 184 HIS E 216 ASN E 285 ASN E 296 ASN E 312 ASN D 53 ASN D 64 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN D 159 HIS F 53 ASN F 104 ASN F 146 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10824 Z= 0.251 Angle : 0.584 7.472 14685 Z= 0.310 Chirality : 0.044 0.194 1650 Planarity : 0.004 0.038 1917 Dihedral : 5.326 45.651 1569 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.68 (0.21), residues: 1323 helix: 1.61 (0.24), residues: 399 sheet: 0.27 (0.35), residues: 246 loop : -2.14 (0.18), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 180 HIS 0.007 0.001 HIS F 106 PHE 0.028 0.002 PHE B 70 TYR 0.021 0.002 TYR B 83 ARG 0.005 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 79 PHE cc_start: 0.8864 (m-80) cc_final: 0.8562 (m-80) REVERT: A 137 ASN cc_start: 0.9498 (m-40) cc_final: 0.8860 (p0) REVERT: A 233 TYR cc_start: 0.8169 (m-80) cc_final: 0.7889 (m-80) REVERT: B 54 ARG cc_start: 0.9475 (mtp85) cc_final: 0.8824 (mtp85) REVERT: B 58 LYS cc_start: 0.9372 (mtmt) cc_final: 0.9042 (mttm) REVERT: B 62 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8530 (mmmm) REVERT: B 64 HIS cc_start: 0.8976 (m-70) cc_final: 0.8727 (m90) REVERT: B 86 ASP cc_start: 0.8437 (t0) cc_final: 0.7931 (t0) REVERT: B 114 GLU cc_start: 0.9488 (tp30) cc_final: 0.9097 (tp30) REVERT: B 117 LYS cc_start: 0.9808 (tptt) cc_final: 0.9597 (tptp) REVERT: B 133 MET cc_start: 0.7601 (ptt) cc_final: 0.7081 (ppp) REVERT: C 70 LEU cc_start: 0.8067 (tp) cc_final: 0.7641 (mt) REVERT: C 98 TYR cc_start: 0.8979 (t80) cc_final: 0.8326 (t80) REVERT: C 137 ASN cc_start: 0.9574 (m-40) cc_final: 0.9078 (p0) REVERT: C 184 HIS cc_start: 0.8322 (m-70) cc_final: 0.8112 (m90) REVERT: C 233 TYR cc_start: 0.8042 (m-80) cc_final: 0.7754 (m-80) REVERT: E 50 LYS cc_start: 0.8617 (mttt) cc_final: 0.8155 (tptm) REVERT: E 98 TYR cc_start: 0.8600 (t80) cc_final: 0.8101 (t80) REVERT: D 58 LYS cc_start: 0.9453 (mtmt) cc_final: 0.9015 (mttm) REVERT: D 86 ASP cc_start: 0.8502 (t0) cc_final: 0.7981 (t0) REVERT: D 108 ILE cc_start: 0.9708 (mt) cc_final: 0.9492 (tt) REVERT: F 38 LEU cc_start: 0.9545 (pt) cc_final: 0.9297 (pt) REVERT: F 59 THR cc_start: 0.9606 (p) cc_final: 0.8942 (p) REVERT: F 63 PHE cc_start: 0.9404 (m-10) cc_final: 0.9034 (m-80) REVERT: F 86 ASP cc_start: 0.8444 (t0) cc_final: 0.8220 (t0) REVERT: F 117 LYS cc_start: 0.9780 (tptt) cc_final: 0.9570 (tptp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3042 time to fit residues: 80.4314 Evaluate side-chains 136 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS A 184 HIS ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN E 75 HIS E 184 HIS D 64 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN F 159 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10824 Z= 0.209 Angle : 0.561 6.253 14685 Z= 0.300 Chirality : 0.043 0.164 1650 Planarity : 0.004 0.037 1917 Dihedral : 5.157 46.734 1569 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.08 % Allowed : 3.54 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.37 (0.21), residues: 1323 helix: 1.74 (0.24), residues: 408 sheet: 0.26 (0.34), residues: 246 loop : -1.81 (0.19), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 127 HIS 0.010 0.001 HIS D 64 PHE 0.017 0.002 PHE D 70 TYR 0.014 0.001 TYR B 83 ARG 0.009 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9481 (m-40) cc_final: 0.8826 (p0) REVERT: A 153 TRP cc_start: 0.9224 (t60) cc_final: 0.8868 (t-100) REVERT: A 233 TYR cc_start: 0.8149 (m-80) cc_final: 0.7933 (m-80) REVERT: B 54 ARG cc_start: 0.9474 (mtp85) cc_final: 0.8809 (mtp-110) REVERT: B 58 LYS cc_start: 0.9400 (mtmt) cc_final: 0.9107 (ptpt) REVERT: B 64 HIS cc_start: 0.8991 (m170) cc_final: 0.8606 (m-70) REVERT: B 86 ASP cc_start: 0.8530 (t0) cc_final: 0.7982 (t0) REVERT: B 133 MET cc_start: 0.7642 (ptt) cc_final: 0.7097 (ppp) REVERT: C 70 LEU cc_start: 0.7843 (tp) cc_final: 0.7394 (mt) REVERT: C 98 TYR cc_start: 0.8984 (t80) cc_final: 0.8489 (t80) REVERT: C 137 ASN cc_start: 0.9542 (m-40) cc_final: 0.9115 (p0) REVERT: C 233 TYR cc_start: 0.8331 (m-80) cc_final: 0.7781 (m-80) REVERT: E 50 LYS cc_start: 0.8634 (mttt) cc_final: 0.8154 (tptp) REVERT: E 98 TYR cc_start: 0.8755 (t80) cc_final: 0.8207 (t80) REVERT: E 233 TYR cc_start: 0.8410 (m-80) cc_final: 0.8183 (m-80) REVERT: D 54 ARG cc_start: 0.9469 (mtp85) cc_final: 0.8782 (mtp-110) REVERT: D 58 LYS cc_start: 0.9548 (mtmt) cc_final: 0.9247 (mttm) REVERT: D 62 LYS cc_start: 0.9316 (mmtt) cc_final: 0.8922 (mmmt) REVERT: D 86 ASP cc_start: 0.8560 (t0) cc_final: 0.8012 (t0) REVERT: D 108 ILE cc_start: 0.9704 (mt) cc_final: 0.9489 (tt) REVERT: F 39 LYS cc_start: 0.9741 (mmtm) cc_final: 0.9491 (mmtm) REVERT: F 61 GLU cc_start: 0.9103 (pp20) cc_final: 0.8603 (pp20) REVERT: F 62 LYS cc_start: 0.8998 (mmtt) cc_final: 0.8759 (mmtt) REVERT: F 66 ILE cc_start: 0.9703 (mt) cc_final: 0.9434 (mt) REVERT: F 70 PHE cc_start: 0.8767 (m-80) cc_final: 0.8274 (m-80) REVERT: F 86 ASP cc_start: 0.8413 (t0) cc_final: 0.7998 (t0) REVERT: F 133 MET cc_start: 0.7789 (ptt) cc_final: 0.7335 (ptt) outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2960 time to fit residues: 76.8680 Evaluate side-chains 136 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 296 ASN A 312 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN F 104 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10824 Z= 0.229 Angle : 0.562 6.952 14685 Z= 0.298 Chirality : 0.044 0.175 1650 Planarity : 0.004 0.035 1917 Dihedral : 5.163 48.931 1569 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.38 (0.21), residues: 1323 helix: 1.71 (0.25), residues: 408 sheet: 0.03 (0.35), residues: 228 loop : -1.65 (0.19), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 127 HIS 0.004 0.001 HIS F 106 PHE 0.013 0.001 PHE C 258 TYR 0.014 0.001 TYR F 83 ARG 0.007 0.001 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 137 ASN cc_start: 0.9444 (m-40) cc_final: 0.8777 (p0) REVERT: A 233 TYR cc_start: 0.8191 (m-80) cc_final: 0.7781 (m-80) REVERT: B 54 ARG cc_start: 0.9489 (mtp85) cc_final: 0.8805 (mtp-110) REVERT: B 58 LYS cc_start: 0.9439 (mtmt) cc_final: 0.9139 (mttm) REVERT: B 64 HIS cc_start: 0.8947 (m170) cc_final: 0.8575 (m-70) REVERT: B 86 ASP cc_start: 0.8533 (t0) cc_final: 0.7987 (t0) REVERT: B 133 MET cc_start: 0.7723 (ptt) cc_final: 0.7193 (ppp) REVERT: C 70 LEU cc_start: 0.7621 (tp) cc_final: 0.7208 (mt) REVERT: C 98 TYR cc_start: 0.9081 (t80) cc_final: 0.8556 (t80) REVERT: C 137 ASN cc_start: 0.9529 (m-40) cc_final: 0.9115 (p0) REVERT: C 231 SER cc_start: 0.8519 (m) cc_final: 0.8285 (m) REVERT: C 233 TYR cc_start: 0.8327 (m-80) cc_final: 0.7807 (m-80) REVERT: C 261 ARG cc_start: 0.4976 (mtt90) cc_final: 0.3882 (ptt90) REVERT: E 50 LYS cc_start: 0.8680 (mttt) cc_final: 0.8193 (tptp) REVERT: E 98 TYR cc_start: 0.7564 (t80) cc_final: 0.6914 (t80) REVERT: D 54 ARG cc_start: 0.9567 (mtp85) cc_final: 0.8916 (mtp-110) REVERT: D 58 LYS cc_start: 0.9429 (mtmt) cc_final: 0.9134 (mttm) REVERT: D 62 LYS cc_start: 0.9475 (mmtt) cc_final: 0.9264 (mmtt) REVERT: D 67 GLU cc_start: 0.9437 (pt0) cc_final: 0.8934 (pp20) REVERT: D 86 ASP cc_start: 0.8556 (t0) cc_final: 0.8017 (t0) REVERT: D 90 ASP cc_start: 0.8732 (m-30) cc_final: 0.8505 (m-30) REVERT: D 108 ILE cc_start: 0.9701 (mt) cc_final: 0.9494 (tt) REVERT: F 39 LYS cc_start: 0.9738 (mmtm) cc_final: 0.9523 (mmtm) REVERT: F 61 GLU cc_start: 0.9185 (pp20) cc_final: 0.8816 (pp20) REVERT: F 62 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8826 (mmtt) REVERT: F 63 PHE cc_start: 0.9443 (m-10) cc_final: 0.9111 (m-80) REVERT: F 86 ASP cc_start: 0.8468 (t0) cc_final: 0.7882 (t0) REVERT: F 90 ASP cc_start: 0.8989 (m-30) cc_final: 0.8789 (m-30) REVERT: F 133 MET cc_start: 0.7752 (ptt) cc_final: 0.7287 (ptt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2769 time to fit residues: 70.3172 Evaluate side-chains 132 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN C 184 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10824 Z= 0.305 Angle : 0.614 10.222 14685 Z= 0.325 Chirality : 0.045 0.187 1650 Planarity : 0.004 0.034 1917 Dihedral : 5.591 53.715 1569 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.17 % Allowed : 2.36 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.57 (0.21), residues: 1323 helix: 1.49 (0.24), residues: 408 sheet: -0.18 (0.33), residues: 234 loop : -1.69 (0.20), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 127 HIS 0.004 0.001 HIS E 18 PHE 0.013 0.002 PHE C 120 TYR 0.016 0.002 TYR F 83 ARG 0.008 0.001 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9411 (m-40) cc_final: 0.8823 (p0) REVERT: A 233 TYR cc_start: 0.7951 (m-80) cc_final: 0.7539 (m-80) REVERT: B 54 ARG cc_start: 0.9509 (mtp85) cc_final: 0.8790 (mtp-110) REVERT: B 58 LYS cc_start: 0.9452 (mtmt) cc_final: 0.9118 (mttm) REVERT: B 66 ILE cc_start: 0.9722 (mt) cc_final: 0.9385 (mt) REVERT: B 70 PHE cc_start: 0.8898 (m-80) cc_final: 0.7811 (m-80) REVERT: B 86 ASP cc_start: 0.8522 (t0) cc_final: 0.7975 (t0) REVERT: B 90 ASP cc_start: 0.8961 (m-30) cc_final: 0.8706 (m-30) REVERT: B 114 GLU cc_start: 0.9520 (tp30) cc_final: 0.9192 (tp30) REVERT: B 133 MET cc_start: 0.7847 (ptt) cc_final: 0.7490 (ppp) REVERT: C 70 LEU cc_start: 0.7578 (tp) cc_final: 0.7225 (mt) REVERT: C 98 TYR cc_start: 0.9124 (t80) cc_final: 0.8584 (t80) REVERT: C 231 SER cc_start: 0.8572 (m) cc_final: 0.8033 (m) REVERT: C 233 TYR cc_start: 0.8390 (m-80) cc_final: 0.7917 (m-80) REVERT: E 50 LYS cc_start: 0.8745 (mttt) cc_final: 0.8269 (tptm) REVERT: E 233 TYR cc_start: 0.8358 (m-80) cc_final: 0.8139 (m-80) REVERT: D 42 GLN cc_start: 0.9627 (mt0) cc_final: 0.9351 (mt0) REVERT: D 54 ARG cc_start: 0.9507 (mtp85) cc_final: 0.8895 (mtp-110) REVERT: D 58 LYS cc_start: 0.9462 (mtmt) cc_final: 0.9206 (mttm) REVERT: D 63 PHE cc_start: 0.9347 (m-10) cc_final: 0.9104 (m-80) REVERT: D 67 GLU cc_start: 0.9418 (pt0) cc_final: 0.8917 (pp20) REVERT: D 86 ASP cc_start: 0.8556 (t0) cc_final: 0.8048 (t0) REVERT: D 90 ASP cc_start: 0.8813 (m-30) cc_final: 0.8530 (m-30) REVERT: D 108 ILE cc_start: 0.9714 (mt) cc_final: 0.9506 (tt) REVERT: F 39 LYS cc_start: 0.9734 (mmtm) cc_final: 0.9527 (mmtm) REVERT: F 59 THR cc_start: 0.9611 (p) cc_final: 0.9060 (p) REVERT: F 62 LYS cc_start: 0.9143 (mmtt) cc_final: 0.8934 (mmtt) REVERT: F 63 PHE cc_start: 0.9464 (m-10) cc_final: 0.9154 (m-80) REVERT: F 66 ILE cc_start: 0.9711 (mt) cc_final: 0.9188 (mt) REVERT: F 70 PHE cc_start: 0.8846 (m-80) cc_final: 0.8048 (m-80) REVERT: F 133 MET cc_start: 0.7824 (ptt) cc_final: 0.7505 (ppp) outliers start: 2 outliers final: 1 residues processed: 186 average time/residue: 0.2902 time to fit residues: 71.3758 Evaluate side-chains 134 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN C 184 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS ** E 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10824 Z= 0.245 Angle : 0.587 8.674 14685 Z= 0.309 Chirality : 0.045 0.174 1650 Planarity : 0.004 0.035 1917 Dihedral : 5.197 46.048 1569 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.46 (0.22), residues: 1323 helix: 1.66 (0.25), residues: 408 sheet: -0.35 (0.32), residues: 246 loop : -1.60 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 153 HIS 0.004 0.001 HIS F 159 PHE 0.029 0.002 PHE B 70 TYR 0.011 0.001 TYR F 83 ARG 0.007 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7983 (t80) cc_final: 0.7702 (t80) REVERT: A 137 ASN cc_start: 0.9332 (m-40) cc_final: 0.8695 (p0) REVERT: A 233 TYR cc_start: 0.7979 (m-80) cc_final: 0.7591 (m-80) REVERT: B 64 HIS cc_start: 0.8943 (m170) cc_final: 0.8618 (m90) REVERT: B 86 ASP cc_start: 0.8468 (t0) cc_final: 0.7946 (t0) REVERT: B 90 ASP cc_start: 0.8937 (m-30) cc_final: 0.8704 (m-30) REVERT: B 118 LEU cc_start: 0.9745 (pp) cc_final: 0.9403 (pp) REVERT: B 133 MET cc_start: 0.7820 (ptt) cc_final: 0.7485 (ppp) REVERT: C 70 LEU cc_start: 0.7592 (tp) cc_final: 0.7272 (mt) REVERT: C 98 TYR cc_start: 0.9132 (t80) cc_final: 0.8604 (t80) REVERT: C 231 SER cc_start: 0.8529 (m) cc_final: 0.8113 (m) REVERT: C 233 TYR cc_start: 0.8373 (m-80) cc_final: 0.7951 (m-80) REVERT: C 261 ARG cc_start: 0.4545 (mtt90) cc_final: 0.2928 (ppt170) REVERT: E 50 LYS cc_start: 0.8760 (mttt) cc_final: 0.8297 (tptm) REVERT: E 233 TYR cc_start: 0.8369 (m-80) cc_final: 0.8140 (m-80) REVERT: D 42 GLN cc_start: 0.9623 (mt0) cc_final: 0.9414 (mp10) REVERT: D 54 ARG cc_start: 0.9519 (mtp85) cc_final: 0.8860 (mtp-110) REVERT: D 58 LYS cc_start: 0.9366 (mtmt) cc_final: 0.9150 (mttm) REVERT: D 78 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8815 (mm110) REVERT: D 86 ASP cc_start: 0.8527 (t0) cc_final: 0.8025 (t0) REVERT: D 90 ASP cc_start: 0.8781 (m-30) cc_final: 0.8509 (m-30) REVERT: F 62 LYS cc_start: 0.9198 (mmtt) cc_final: 0.8868 (mmtp) REVERT: F 63 PHE cc_start: 0.9401 (m-10) cc_final: 0.8990 (m-80) REVERT: F 86 ASP cc_start: 0.8452 (t0) cc_final: 0.7847 (t0) REVERT: F 90 ASP cc_start: 0.9023 (m-30) cc_final: 0.8776 (m-30) REVERT: F 133 MET cc_start: 0.7844 (ptt) cc_final: 0.7504 (ppp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2706 time to fit residues: 65.1572 Evaluate side-chains 124 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 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 184 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 105 GLN C 184 HIS E 184 HIS D 104 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10824 Z= 0.182 Angle : 0.572 7.797 14685 Z= 0.301 Chirality : 0.044 0.195 1650 Planarity : 0.004 0.034 1917 Dihedral : 4.881 41.499 1569 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1323 helix: 1.80 (0.25), residues: 408 sheet: -0.18 (0.36), residues: 192 loop : -1.34 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 153 HIS 0.004 0.001 HIS F 159 PHE 0.056 0.001 PHE B 70 TYR 0.008 0.001 TYR F 157 ARG 0.006 0.000 ARG F 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8089 (t80) cc_final: 0.7799 (t80) REVERT: A 137 ASN cc_start: 0.9304 (m-40) cc_final: 0.8636 (p0) REVERT: A 233 TYR cc_start: 0.8011 (m-80) cc_final: 0.7572 (m-80) REVERT: B 64 HIS cc_start: 0.8870 (m170) cc_final: 0.8586 (m-70) REVERT: B 65 GLN cc_start: 0.9020 (pm20) cc_final: 0.8815 (pm20) REVERT: B 86 ASP cc_start: 0.8516 (t0) cc_final: 0.8027 (t0) REVERT: B 118 LEU cc_start: 0.9714 (pp) cc_final: 0.9488 (pp) REVERT: B 133 MET cc_start: 0.7802 (ptt) cc_final: 0.7319 (ppp) REVERT: C 70 LEU cc_start: 0.7540 (tp) cc_final: 0.7248 (mt) REVERT: C 98 TYR cc_start: 0.9122 (t80) cc_final: 0.8640 (t80) REVERT: C 231 SER cc_start: 0.8485 (m) cc_final: 0.8072 (m) REVERT: C 233 TYR cc_start: 0.8321 (m-80) cc_final: 0.7940 (m-80) REVERT: E 50 LYS cc_start: 0.8728 (mttt) cc_final: 0.8267 (tptm) REVERT: E 233 TYR cc_start: 0.8358 (m-80) cc_final: 0.8127 (m-80) REVERT: D 42 GLN cc_start: 0.9612 (mt0) cc_final: 0.9403 (mp10) REVERT: D 54 ARG cc_start: 0.9512 (mtp85) cc_final: 0.8901 (mtp-110) REVERT: D 63 PHE cc_start: 0.9299 (m-10) cc_final: 0.8957 (m-80) REVERT: D 70 PHE cc_start: 0.8551 (m-80) cc_final: 0.8304 (m-80) REVERT: D 86 ASP cc_start: 0.8505 (t0) cc_final: 0.7993 (t0) REVERT: D 90 ASP cc_start: 0.8741 (m-30) cc_final: 0.8475 (m-30) REVERT: D 108 ILE cc_start: 0.9714 (mt) cc_final: 0.9447 (tt) REVERT: F 59 THR cc_start: 0.9627 (p) cc_final: 0.8987 (p) REVERT: F 63 PHE cc_start: 0.9394 (m-10) cc_final: 0.9037 (m-80) REVERT: F 66 ILE cc_start: 0.9590 (mt) cc_final: 0.9090 (mt) REVERT: F 70 PHE cc_start: 0.8443 (m-80) cc_final: 0.7841 (m-80) REVERT: F 86 ASP cc_start: 0.8439 (t0) cc_final: 0.7814 (t0) REVERT: F 90 ASP cc_start: 0.8940 (m-30) cc_final: 0.8726 (m-30) REVERT: F 133 MET cc_start: 0.7796 (ptt) cc_final: 0.7472 (ppp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2550 time to fit residues: 62.2082 Evaluate side-chains 133 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 0.3980 chunk 115 optimal weight: 8.9990 chunk 121 optimal weight: 0.0020 chunk 111 optimal weight: 1.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 298 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 184 HIS D 104 ASN D 105 GLN F 104 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10824 Z= 0.195 Angle : 0.573 7.797 14685 Z= 0.302 Chirality : 0.044 0.176 1650 Planarity : 0.004 0.035 1917 Dihedral : 4.817 40.712 1569 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.13 (0.22), residues: 1323 helix: 1.89 (0.25), residues: 408 sheet: -0.08 (0.37), residues: 186 loop : -1.31 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 153 HIS 0.006 0.001 HIS D 106 PHE 0.049 0.001 PHE B 70 TYR 0.008 0.001 TYR F 157 ARG 0.007 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8195 (t80) cc_final: 0.7848 (t80) REVERT: A 137 ASN cc_start: 0.9313 (m-40) cc_final: 0.8667 (p0) REVERT: A 233 TYR cc_start: 0.8073 (m-80) cc_final: 0.7667 (m-80) REVERT: B 64 HIS cc_start: 0.8830 (m170) cc_final: 0.8595 (m-70) REVERT: B 65 GLN cc_start: 0.8965 (pm20) cc_final: 0.8734 (pm20) REVERT: B 86 ASP cc_start: 0.8549 (t0) cc_final: 0.8002 (t0) REVERT: B 90 ASP cc_start: 0.8879 (m-30) cc_final: 0.8652 (m-30) REVERT: B 114 GLU cc_start: 0.9382 (tp30) cc_final: 0.9175 (tp30) REVERT: B 118 LEU cc_start: 0.9771 (pp) cc_final: 0.9350 (pp) REVERT: B 133 MET cc_start: 0.7747 (ptt) cc_final: 0.7437 (ppp) REVERT: C 70 LEU cc_start: 0.7589 (tp) cc_final: 0.7315 (mt) REVERT: C 98 TYR cc_start: 0.9137 (t80) cc_final: 0.8611 (t80) REVERT: C 231 SER cc_start: 0.8470 (m) cc_final: 0.8066 (m) REVERT: C 233 TYR cc_start: 0.8343 (m-80) cc_final: 0.7981 (m-80) REVERT: E 233 TYR cc_start: 0.8372 (m-80) cc_final: 0.8147 (m-80) REVERT: D 42 GLN cc_start: 0.9618 (mt0) cc_final: 0.9412 (mp10) REVERT: D 63 PHE cc_start: 0.9339 (m-10) cc_final: 0.9039 (m-80) REVERT: D 70 PHE cc_start: 0.8492 (m-80) cc_final: 0.8281 (m-80) REVERT: D 86 ASP cc_start: 0.8510 (t0) cc_final: 0.8007 (t0) REVERT: D 90 ASP cc_start: 0.8743 (m-30) cc_final: 0.8467 (m-30) REVERT: D 108 ILE cc_start: 0.9721 (mt) cc_final: 0.9462 (tt) REVERT: F 59 THR cc_start: 0.9635 (p) cc_final: 0.9030 (p) REVERT: F 63 PHE cc_start: 0.9402 (m-10) cc_final: 0.9056 (m-80) REVERT: F 66 ILE cc_start: 0.9607 (mt) cc_final: 0.9092 (mt) REVERT: F 70 PHE cc_start: 0.8395 (m-80) cc_final: 0.7794 (m-80) REVERT: F 86 ASP cc_start: 0.8438 (t0) cc_final: 0.7818 (t0) REVERT: F 90 ASP cc_start: 0.8941 (m-30) cc_final: 0.8718 (m-30) REVERT: F 133 MET cc_start: 0.7730 (ptt) cc_final: 0.7419 (ppp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2616 time to fit residues: 62.2646 Evaluate side-chains 128 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 184 HIS D 78 GLN D 104 ASN F 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10824 Z= 0.181 Angle : 0.592 12.395 14685 Z= 0.311 Chirality : 0.045 0.171 1650 Planarity : 0.004 0.048 1917 Dihedral : 4.649 37.752 1569 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.11 (0.22), residues: 1323 helix: 1.93 (0.25), residues: 408 sheet: -0.18 (0.36), residues: 204 loop : -1.30 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 153 HIS 0.008 0.001 HIS D 106 PHE 0.056 0.001 PHE B 70 TYR 0.008 0.001 TYR F 157 ARG 0.010 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8243 (t80) cc_final: 0.7864 (t80) REVERT: A 137 ASN cc_start: 0.9312 (m-40) cc_final: 0.8666 (p0) REVERT: A 233 TYR cc_start: 0.8023 (m-80) cc_final: 0.7639 (m-80) REVERT: B 58 LYS cc_start: 0.9407 (mtmt) cc_final: 0.9015 (mttm) REVERT: B 64 HIS cc_start: 0.8829 (m170) cc_final: 0.8495 (m90) REVERT: B 86 ASP cc_start: 0.8539 (t0) cc_final: 0.7996 (t0) REVERT: B 90 ASP cc_start: 0.8885 (m-30) cc_final: 0.8670 (m-30) REVERT: B 115 MET cc_start: 0.9051 (tpt) cc_final: 0.8824 (ttt) REVERT: B 118 LEU cc_start: 0.9729 (pp) cc_final: 0.9328 (pp) REVERT: B 133 MET cc_start: 0.7726 (ptt) cc_final: 0.7430 (ppp) REVERT: C 70 LEU cc_start: 0.7542 (tp) cc_final: 0.7280 (mt) REVERT: C 98 TYR cc_start: 0.9148 (t80) cc_final: 0.8623 (t80) REVERT: C 231 SER cc_start: 0.8534 (m) cc_final: 0.8112 (m) REVERT: C 233 TYR cc_start: 0.8335 (m-80) cc_final: 0.7994 (m-80) REVERT: E 98 TYR cc_start: 0.8382 (t80) cc_final: 0.8156 (t80) REVERT: E 233 TYR cc_start: 0.8326 (m-80) cc_final: 0.8112 (m-80) REVERT: D 42 GLN cc_start: 0.9611 (mt0) cc_final: 0.9399 (mp10) REVERT: D 54 ARG cc_start: 0.9486 (mtp85) cc_final: 0.9191 (mtp-110) REVERT: D 63 PHE cc_start: 0.9358 (m-10) cc_final: 0.9028 (m-80) REVERT: D 69 GLU cc_start: 0.9122 (mp0) cc_final: 0.8842 (mp0) REVERT: D 86 ASP cc_start: 0.8503 (t0) cc_final: 0.7969 (t0) REVERT: D 90 ASP cc_start: 0.8698 (m-30) cc_final: 0.8431 (m-30) REVERT: F 63 PHE cc_start: 0.9408 (m-10) cc_final: 0.8965 (m-80) REVERT: F 70 PHE cc_start: 0.8438 (m-80) cc_final: 0.8140 (m-80) REVERT: F 86 ASP cc_start: 0.8462 (t0) cc_final: 0.7831 (t0) REVERT: F 90 ASP cc_start: 0.8932 (m-30) cc_final: 0.8716 (m-30) REVERT: F 133 MET cc_start: 0.7709 (ptt) cc_final: 0.7411 (ppp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2628 time to fit residues: 64.1654 Evaluate side-chains 134 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 184 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10824 Z= 0.196 Angle : 0.631 11.175 14685 Z= 0.336 Chirality : 0.045 0.179 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.665 37.765 1569 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.12 (0.22), residues: 1323 helix: 1.84 (0.25), residues: 408 sheet: -0.09 (0.36), residues: 204 loop : -1.28 (0.21), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 153 HIS 0.009 0.001 HIS F 106 PHE 0.061 0.002 PHE B 70 TYR 0.008 0.001 TYR F 162 ARG 0.018 0.001 ARG D 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8289 (t80) cc_final: 0.7882 (t80) REVERT: A 137 ASN cc_start: 0.9304 (m-40) cc_final: 0.8657 (p0) REVERT: A 233 TYR cc_start: 0.8053 (m-80) cc_final: 0.7656 (m-80) REVERT: B 64 HIS cc_start: 0.8838 (m170) cc_final: 0.8546 (m-70) REVERT: B 65 GLN cc_start: 0.9181 (pm20) cc_final: 0.8931 (pm20) REVERT: B 86 ASP cc_start: 0.8519 (t0) cc_final: 0.7967 (t0) REVERT: B 90 ASP cc_start: 0.8862 (m-30) cc_final: 0.8629 (m-30) REVERT: B 115 MET cc_start: 0.9036 (tpt) cc_final: 0.8802 (ttt) REVERT: B 118 LEU cc_start: 0.9732 (pp) cc_final: 0.9329 (pp) REVERT: B 133 MET cc_start: 0.7710 (ptt) cc_final: 0.7450 (ppp) REVERT: C 70 LEU cc_start: 0.7548 (tp) cc_final: 0.7179 (mt) REVERT: C 98 TYR cc_start: 0.9159 (t80) cc_final: 0.8641 (t80) REVERT: C 231 SER cc_start: 0.8492 (m) cc_final: 0.8053 (m) REVERT: C 233 TYR cc_start: 0.8394 (m-80) cc_final: 0.8006 (m-80) REVERT: E 50 LYS cc_start: 0.8732 (mttt) cc_final: 0.8233 (tttp) REVERT: E 233 TYR cc_start: 0.8347 (m-80) cc_final: 0.8128 (m-80) REVERT: D 42 GLN cc_start: 0.9611 (mt0) cc_final: 0.9401 (mp10) REVERT: D 54 ARG cc_start: 0.9480 (mtp85) cc_final: 0.9161 (mtp-110) REVERT: D 63 PHE cc_start: 0.9395 (m-10) cc_final: 0.9077 (m-80) REVERT: D 66 ILE cc_start: 0.9754 (mt) cc_final: 0.9423 (mt) REVERT: D 69 GLU cc_start: 0.9124 (mp0) cc_final: 0.8831 (mp0) REVERT: D 70 PHE cc_start: 0.8472 (m-80) cc_final: 0.8023 (m-80) REVERT: D 86 ASP cc_start: 0.8503 (t0) cc_final: 0.7975 (t0) REVERT: D 90 ASP cc_start: 0.8741 (m-30) cc_final: 0.8473 (m-30) REVERT: F 59 THR cc_start: 0.9619 (p) cc_final: 0.8918 (p) REVERT: F 63 PHE cc_start: 0.9411 (m-10) cc_final: 0.8969 (m-80) REVERT: F 70 PHE cc_start: 0.8420 (m-80) cc_final: 0.7887 (m-80) REVERT: F 86 ASP cc_start: 0.8431 (t0) cc_final: 0.7810 (t0) REVERT: F 90 ASP cc_start: 0.8933 (m-30) cc_final: 0.8719 (m-30) REVERT: F 133 MET cc_start: 0.7728 (ptt) cc_final: 0.7431 (ppp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2617 time to fit residues: 61.7684 Evaluate side-chains 135 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 184 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.082512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055383 restraints weight = 47310.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054548 restraints weight = 23967.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055080 restraints weight = 21535.254| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10824 Z= 0.184 Angle : 0.603 11.506 14685 Z= 0.317 Chirality : 0.045 0.190 1650 Planarity : 0.004 0.037 1917 Dihedral : 4.513 35.430 1569 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.01 (0.22), residues: 1323 helix: 1.89 (0.25), residues: 408 sheet: 0.04 (0.37), residues: 204 loop : -1.21 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 222 HIS 0.007 0.001 HIS F 106 PHE 0.059 0.002 PHE B 70 TYR 0.006 0.001 TYR C 257 ARG 0.004 0.000 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.18 seconds wall clock time: 44 minutes 7.16 seconds (2647.16 seconds total)