Starting phenix.real_space_refine on Wed Nov 15 04:16:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjy_22902/11_2023/7kjy_22902_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjy_22902/11_2023/7kjy_22902.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/7kjy_22902/11_2023/7kjy_22902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjy_22902/11_2023/7kjy_22902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjy_22902/11_2023/7kjy_22902_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kjy_22902/11_2023/7kjy_22902_updated.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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 8 5.49 5 S 56 5.16 5 C 6632 2.51 5 N 1780 2.21 5 O 2024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 10508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "D" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 2, 'NAD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 38.026 59.693 54.887 1.00141.59 S ATOM 1158 SG CYS A 153 39.083 56.108 52.991 1.00113.64 S ATOM 747 SG CYS A 97 32.022 48.850 34.077 1.00138.02 S ATOM 766 SG CYS A 100 36.101 49.335 33.968 1.00133.66 S ATOM 793 SG CYS A 103 35.139 47.934 36.928 1.00130.51 S ATOM 851 SG CYS A 111 33.795 51.117 36.047 1.00131.41 S ATOM 2921 SG CYS B 43 75.493 59.543 24.902 1.00140.20 S ATOM 3739 SG CYS B 153 74.435 55.963 26.806 1.00114.33 S ATOM 3328 SG CYS B 97 81.440 48.722 45.750 1.00138.47 S ATOM 3347 SG CYS B 100 77.380 49.199 45.948 1.00133.10 S ATOM 3374 SG CYS B 103 78.378 47.852 42.892 1.00129.21 S ATOM 3432 SG CYS B 111 79.743 50.995 43.754 1.00130.34 S ATOM 5502 SG CYS C 43 75.276 22.259 55.034 1.00141.93 S ATOM 6320 SG CYS C 153 74.244 25.844 53.125 1.00114.20 S ATOM 5909 SG CYS C 97 81.394 32.997 34.191 1.00137.88 S ATOM 5928 SG CYS C 100 77.315 32.593 34.000 1.00133.54 S ATOM 5955 SG CYS C 103 78.332 33.986 37.029 1.00130.48 S ATOM 6013 SG CYS C 111 79.626 30.794 36.172 1.00131.13 S ATOM 8083 SG CYS D 43 37.973 22.298 24.761 1.00140.99 S ATOM 8901 SG CYS D 153 39.015 25.881 26.668 1.00112.42 S ATOM 8490 SG CYS D 97 31.993 33.121 45.633 1.00136.84 S ATOM 8509 SG CYS D 100 36.045 32.650 45.895 1.00131.86 S ATOM 8536 SG CYS D 103 35.028 33.949 42.787 1.00129.36 S ATOM 8594 SG CYS D 111 33.682 30.817 43.630 1.00129.47 S Time building chain proxies: 5.92, per 1000 atoms: 0.56 Number of scatterers: 10508 At special positions: 0 Unit cell: (114.45, 82.95, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 56 16.00 P 8 15.00 O 2024 8.00 N 1780 7.00 C 6632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS B 277 " distance=1.93 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS D 277 " distance=2.14 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: 4.59 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 16 sheets defined 28.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 145 through 152 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 181 through 193 removed outlier: 4.137A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 145 through 152 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 154 through 165 Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.137A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 325 through 333 Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 102 through 105 No H-bonds generated for 'chain 'C' and resid 102 through 105' Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 145 through 152 Proline residue: C 150 - end of helix Processing helix chain 'C' and resid 154 through 165 Processing helix chain 'C' and resid 181 through 193 removed outlier: 4.138A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 227 through 235 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 298 through 309 Processing helix chain 'C' and resid 325 through 333 Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 102 through 105 No H-bonds generated for 'chain 'D' and resid 102 through 105' Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 145 through 152 Proline residue: D 150 - end of helix Processing helix chain 'D' and resid 154 through 165 Processing helix chain 'D' and resid 181 through 193 removed outlier: 4.138A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 325 through 333 Processing sheet with id= A, first strand: chain 'A' and resid 5 through 10 Processing sheet with id= B, first strand: chain 'A' and resid 128 through 132 removed outlier: 4.044A pdb=" N GLY A 74 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN A 36 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL A 72 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 87 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 39 through 41 removed outlier: 4.528A pdb=" N GLU A 67 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 264 through 267 removed outlier: 5.955A pdb=" N ARG A 196 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE A 175 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 198 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 217 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP A 201 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ILE A 219 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 5 through 10 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.043A pdb=" N GLY B 74 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASN B 36 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL B 72 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR B 87 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 39 through 41 removed outlier: 4.528A pdb=" N GLU B 67 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 264 through 267 removed outlier: 5.954A pdb=" N ARG B 196 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 175 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 198 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 217 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ASP B 201 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE B 219 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 5 through 10 Processing sheet with id= J, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.043A pdb=" N GLY C 74 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN C 36 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL C 72 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR C 87 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 39 through 41 removed outlier: 4.528A pdb=" N GLU C 67 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 264 through 267 removed outlier: 5.954A pdb=" N ARG C 196 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 175 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 198 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 217 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP C 201 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE C 219 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 Processing sheet with id= N, first strand: chain 'D' and resid 128 through 132 removed outlier: 4.043A pdb=" N GLY D 74 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN D 36 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL D 72 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR D 87 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.529A pdb=" N GLU D 67 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 264 through 267 removed outlier: 5.954A pdb=" N ARG D 196 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE D 175 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU D 198 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 217 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASP D 201 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE D 219 " --> pdb=" O ASP D 201 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 867 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: 2.77 Time building geometry restraints manager: 4.76 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: 3374 1.34 - 1.45: 1857 1.45 - 1.57: 5405 1.57 - 1.69: 16 1.69 - 1.81: 80 Bond restraints: 10732 Sorted by residual: bond pdb=" O3 NAD B 403 " pdb=" PA NAD B 403 " ideal model delta sigma weight residual 1.653 1.597 0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" O3 NAD A 403 " pdb=" PA NAD A 403 " ideal model delta sigma weight residual 1.653 1.597 0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" O3 NAD C 403 " pdb=" PA NAD C 403 " ideal model delta sigma weight residual 1.653 1.597 0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" O3 NAD D 403 " pdb=" PA NAD D 403 " ideal model delta sigma weight residual 1.653 1.598 0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" N SER D 96 " pdb=" CA SER D 96 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.60e+00 ... (remaining 10727 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.36: 343 106.36 - 113.27: 5963 113.27 - 120.17: 3725 120.17 - 127.07: 4409 127.07 - 133.97: 140 Bond angle restraints: 14580 Sorted by residual: angle pdb=" CA MET D 98 " pdb=" C MET D 98 " pdb=" O MET D 98 " ideal model delta sigma weight residual 121.54 117.56 3.98 1.16e+00 7.43e-01 1.17e+01 angle pdb=" CA MET C 98 " pdb=" C MET C 98 " pdb=" O MET C 98 " ideal model delta sigma weight residual 121.54 117.59 3.95 1.16e+00 7.43e-01 1.16e+01 angle pdb=" CA SER D 96 " pdb=" C SER D 96 " pdb=" O SER D 96 " ideal model delta sigma weight residual 121.89 117.73 4.16 1.27e+00 6.20e-01 1.07e+01 angle pdb=" CA MET B 98 " pdb=" C MET B 98 " pdb=" O MET B 98 " ideal model delta sigma weight residual 121.54 117.74 3.80 1.16e+00 7.43e-01 1.07e+01 angle pdb=" CA MET A 98 " pdb=" C MET A 98 " pdb=" O MET A 98 " ideal model delta sigma weight residual 121.54 117.79 3.75 1.16e+00 7.43e-01 1.04e+01 ... (remaining 14575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5516 17.41 - 34.82: 520 34.82 - 52.23: 118 52.23 - 69.64: 24 69.64 - 87.05: 20 Dihedral angle restraints: 6198 sinusoidal: 2334 harmonic: 3864 Sorted by residual: dihedral pdb=" CA ASP B 220 " pdb=" CB ASP B 220 " pdb=" CG ASP B 220 " pdb=" OD1 ASP B 220 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP D 220 " pdb=" CB ASP D 220 " pdb=" CG ASP D 220 " pdb=" OD1 ASP D 220 " ideal model delta sinusoidal sigma weight residual -30.00 -88.57 58.57 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 220 " pdb=" CB ASP A 220 " pdb=" CG ASP A 220 " pdb=" OD1 ASP A 220 " ideal model delta sinusoidal sigma weight residual -30.00 -88.55 58.55 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 6195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1304 0.056 - 0.113: 279 0.113 - 0.169: 26 0.169 - 0.226: 3 0.226 - 0.282: 12 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA CYS D 111 " pdb=" N CYS D 111 " pdb=" C CYS D 111 " pdb=" CB CYS D 111 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA CYS B 111 " pdb=" N CYS B 111 " pdb=" C CYS B 111 " pdb=" CB CYS B 111 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA CYS A 111 " pdb=" N CYS A 111 " pdb=" C CYS A 111 " pdb=" CB CYS A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1621 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 403 " -0.010 2.00e-02 2.50e+03 1.76e-02 6.22e+00 pdb=" C2N NAD A 403 " -0.017 2.00e-02 2.50e+03 pdb=" C3N NAD A 403 " -0.006 2.00e-02 2.50e+03 pdb=" C4N NAD A 403 " -0.025 2.00e-02 2.50e+03 pdb=" C5N NAD A 403 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAD A 403 " 0.029 2.00e-02 2.50e+03 pdb=" C7N NAD A 403 " 0.023 2.00e-02 2.50e+03 pdb=" N1N NAD A 403 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 403 " 0.010 2.00e-02 2.50e+03 1.75e-02 6.12e+00 pdb=" C2N NAD B 403 " 0.017 2.00e-02 2.50e+03 pdb=" C3N NAD B 403 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD B 403 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD B 403 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD B 403 " -0.029 2.00e-02 2.50e+03 pdb=" C7N NAD B 403 " -0.023 2.00e-02 2.50e+03 pdb=" N1N NAD B 403 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 403 " -0.010 2.00e-02 2.50e+03 1.75e-02 6.11e+00 pdb=" C2N NAD D 403 " -0.017 2.00e-02 2.50e+03 pdb=" C3N NAD D 403 " -0.006 2.00e-02 2.50e+03 pdb=" C4N NAD D 403 " -0.025 2.00e-02 2.50e+03 pdb=" C5N NAD D 403 " -0.002 2.00e-02 2.50e+03 pdb=" C6N NAD D 403 " 0.029 2.00e-02 2.50e+03 pdb=" C7N NAD D 403 " 0.023 2.00e-02 2.50e+03 pdb=" N1N NAD D 403 " 0.008 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 676 2.72 - 3.26: 11623 3.26 - 3.81: 18237 3.81 - 4.35: 22579 4.35 - 4.90: 38115 Nonbonded interactions: 91230 Sorted by model distance: nonbonded pdb=" OD2 ASP B 201 " pdb=" O3B NAD B 403 " model vdw 2.169 2.440 nonbonded pdb=" OD2 ASP D 201 " pdb=" O3B NAD D 403 " model vdw 2.169 2.440 nonbonded pdb=" OD2 ASP C 201 " pdb=" O3B NAD C 403 " model vdw 2.170 2.440 nonbonded pdb=" OD2 ASP A 201 " pdb=" O3B NAD A 403 " model vdw 2.170 2.440 nonbonded pdb=" OD1 ASP B 220 " pdb=" N LYS B 223 " model vdw 2.282 2.520 ... (remaining 91225 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 'B' selection = chain 'C' selection = chain 'D' } 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.820 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 33.210 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.007 0.056 10732 Z= 0.459 Angle : 0.707 10.025 14580 Z= 0.380 Chirality : 0.051 0.282 1624 Planarity : 0.003 0.030 1856 Dihedral : 15.155 87.055 3768 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.48 % Allowed : 13.62 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.91 (0.17), residues: 1380 helix: -1.72 (0.19), residues: 448 sheet: -3.68 (0.23), residues: 212 loop : -2.85 (0.17), residues: 720 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 90 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 134 average time/residue: 0.3090 time to fit residues: 54.8263 Evaluate side-chains 75 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0968 time to fit residues: 5.3669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 overall best weight: 2.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 51 HIS ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 51 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS C 51 HIS ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 HIS D 51 HIS ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10732 Z= 0.249 Angle : 0.549 8.026 14580 Z= 0.257 Chirality : 0.043 0.141 1624 Planarity : 0.003 0.036 1856 Dihedral : 5.257 51.782 1496 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.49 % Allowed : 17.54 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.19 (0.20), residues: 1380 helix: -0.05 (0.23), residues: 448 sheet: -2.96 (0.26), residues: 240 loop : -1.81 (0.21), residues: 692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 75 average time/residue: 0.2748 time to fit residues: 28.9785 Evaluate side-chains 48 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0969 time to fit residues: 2.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 123 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 10732 Z= 0.425 Angle : 0.611 8.848 14580 Z= 0.288 Chirality : 0.044 0.130 1624 Planarity : 0.004 0.036 1856 Dihedral : 4.879 45.086 1496 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.45 % Allowed : 18.19 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.82 (0.21), residues: 1380 helix: 0.37 (0.24), residues: 448 sheet: -2.94 (0.26), residues: 248 loop : -1.56 (0.22), residues: 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 41 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 74 average time/residue: 0.2359 time to fit residues: 26.3074 Evaluate side-chains 55 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 34 time to evaluate : 1.319 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1102 time to fit residues: 5.8463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10732 Z= 0.253 Angle : 0.529 7.296 14580 Z= 0.254 Chirality : 0.042 0.136 1624 Planarity : 0.003 0.034 1856 Dihedral : 4.600 41.595 1496 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.12 % Allowed : 20.62 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.22), residues: 1380 helix: 0.80 (0.25), residues: 448 sheet: -2.90 (0.25), residues: 280 loop : -0.98 (0.24), residues: 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 48 average time/residue: 0.2186 time to fit residues: 16.7691 Evaluate side-chains 42 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 1.351 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1177 time to fit residues: 3.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10732 Z= 0.360 Angle : 0.555 7.990 14580 Z= 0.268 Chirality : 0.044 0.133 1624 Planarity : 0.003 0.032 1856 Dihedral : 4.465 36.692 1496 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.65 % Allowed : 20.90 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.43 (0.22), residues: 1380 helix: 0.71 (0.24), residues: 460 sheet: -3.02 (0.24), residues: 296 loop : -1.01 (0.25), residues: 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 43 average time/residue: 0.2147 time to fit residues: 14.9214 Evaluate side-chains 37 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0964 time to fit residues: 1.6848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10732 Z= 0.278 Angle : 0.509 7.192 14580 Z= 0.248 Chirality : 0.043 0.134 1624 Planarity : 0.003 0.031 1856 Dihedral : 4.368 35.744 1496 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.93 % Allowed : 21.08 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.24 (0.23), residues: 1380 helix: 0.89 (0.25), residues: 460 sheet: -2.89 (0.25), residues: 296 loop : -0.94 (0.25), residues: 624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 46 average time/residue: 0.2139 time to fit residues: 15.7534 Evaluate side-chains 40 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0964 time to fit residues: 2.3218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 0.2980 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10732 Z= 0.256 Angle : 0.496 6.921 14580 Z= 0.242 Chirality : 0.043 0.135 1624 Planarity : 0.003 0.031 1856 Dihedral : 4.298 34.377 1496 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.21 % Allowed : 20.43 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.10 (0.23), residues: 1380 helix: 1.03 (0.25), residues: 460 sheet: -2.81 (0.25), residues: 296 loop : -0.88 (0.25), residues: 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 49 average time/residue: 0.1984 time to fit residues: 15.8069 Evaluate side-chains 40 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0865 time to fit residues: 2.2766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10732 Z= 0.341 Angle : 0.532 7.676 14580 Z= 0.259 Chirality : 0.044 0.131 1624 Planarity : 0.003 0.030 1856 Dihedral : 4.338 32.982 1496 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.75 % Allowed : 20.99 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.91 (0.23), residues: 1380 helix: 0.98 (0.24), residues: 460 sheet: -3.10 (0.29), residues: 232 loop : -0.69 (0.24), residues: 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 44 average time/residue: 0.2109 time to fit residues: 14.9625 Evaluate side-chains 36 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1031 time to fit residues: 1.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 37 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10732 Z= 0.261 Angle : 0.505 6.955 14580 Z= 0.245 Chirality : 0.043 0.163 1624 Planarity : 0.003 0.031 1856 Dihedral : 4.283 32.755 1496 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 22.01 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.79 (0.23), residues: 1380 helix: 1.13 (0.25), residues: 460 sheet: -3.03 (0.29), residues: 232 loop : -0.66 (0.24), residues: 688 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.2932 time to fit residues: 16.4601 Evaluate side-chains 37 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 135 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10732 Z= 0.304 Angle : 0.519 7.322 14580 Z= 0.251 Chirality : 0.043 0.147 1624 Planarity : 0.003 0.033 1856 Dihedral : 4.290 31.843 1496 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.19 % Allowed : 22.01 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.79 (0.23), residues: 1380 helix: 1.12 (0.25), residues: 460 sheet: -3.02 (0.29), residues: 232 loop : -0.66 (0.24), residues: 688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.2997 time to fit residues: 17.1000 Evaluate side-chains 36 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1629 time to fit residues: 1.9700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.061087 restraints weight = 19161.990| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.11 r_work: 0.2579 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10732 Z= 0.232 Angle : 0.495 6.603 14580 Z= 0.239 Chirality : 0.043 0.141 1624 Planarity : 0.003 0.032 1856 Dihedral : 4.216 32.492 1496 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.09 % Allowed : 22.20 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 (0.23), residues: 1380 helix: 1.23 (0.25), residues: 460 sheet: -2.93 (0.29), residues: 232 loop : -0.62 (0.24), residues: 688 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.16 seconds wall clock time: 34 minutes 22.62 seconds (2062.62 seconds total)