Starting phenix.real_space_refine on Wed Feb 14 02:54:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/02_2024/7wx3_32875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/02_2024/7wx3_32875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/02_2024/7wx3_32875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/02_2024/7wx3_32875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/02_2024/7wx3_32875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/02_2024/7wx3_32875_updated.pdb" } resolution = 3.1 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= 0.006 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 P 12 5.49 5 Mg 4 5.21 5 S 68 5.16 5 C 5296 2.51 5 N 1429 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 307": "OD1" <-> "OD2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ASP 277": "OD1" <-> "OD2" Residue "B ARG 308": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "C ARG 330": "NH1" <-> "NH2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 277": "OD1" <-> "OD2" Residue "D ARG 308": "NH1" <-> "NH2" Residue "D ARG 330": "NH1" <-> "NH2" Residue "H GLU 116": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8472 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1930 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain breaks: 3 Chain: "E" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1974 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Chain: "F" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1974 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Chain: "G" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1974 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 3 Chain: "H" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 113 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Time building chain proxies: 5.03, per 1000 atoms: 0.59 Number of scatterers: 8472 At special positions: 0 Unit cell: (104.94, 92.22, 100.7, 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) S 68 16.00 P 12 15.00 Mg 4 11.99 O 1663 8.00 N 1429 7.00 C 5296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB RGP A 801 " pdb=" CB RGP B 801 " pdb=" CB RGP C 801 " pdb=" CB RGP D 801 " Number of C-beta restraints generated: 2036 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 8 sheets defined 43.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.548A pdb=" N LEU A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 105 through 120 removed outlier: 4.101A pdb=" N SER A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 142 through 164 removed outlier: 4.253A pdb=" N TYR A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.655A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 296 through 307 Processing helix chain 'A' and resid 323 through 326 No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'E' and resid 123 through 126 No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.548A pdb=" N LEU B 53 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS B 54 " --> pdb=" O SER B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.101A pdb=" N SER B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 126 No H-bonds generated for 'chain 'B' and resid 123 through 126' Processing helix chain 'B' and resid 142 through 164 removed outlier: 4.251A pdb=" N TYR B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.656A pdb=" N LEU B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.926A pdb=" N SER B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 323 through 326 No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'F' and resid 123 through 126 No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'C' and resid 50 through 55 removed outlier: 3.532A pdb=" N LEU C 53 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS C 54 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 105 through 120 removed outlier: 4.120A pdb=" N SER C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 142 through 164 removed outlier: 4.254A pdb=" N TYR C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.654A pdb=" N LEU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.915A pdb=" N SER C 281 " --> pdb=" O ASP C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 307 Processing helix chain 'C' and resid 323 through 326 No H-bonds generated for 'chain 'C' and resid 323 through 326' Processing helix chain 'G' and resid 123 through 126 No H-bonds generated for 'chain 'G' and resid 123 through 126' Processing helix chain 'D' and resid 50 through 55 removed outlier: 3.530A pdb=" N LEU D 53 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.107A pdb=" N SER D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 No H-bonds generated for 'chain 'D' and resid 123 through 126' Processing helix chain 'D' and resid 142 through 164 removed outlier: 4.253A pdb=" N TYR D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.651A pdb=" N LEU D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 243 Processing helix chain 'D' and resid 276 through 281 removed outlier: 3.897A pdb=" N SER D 281 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 307 Processing helix chain 'D' and resid 323 through 326 No H-bonds generated for 'chain 'D' and resid 323 through 326' Processing helix chain 'H' and resid 123 through 126 No H-bonds generated for 'chain 'H' and resid 123 through 126' Processing sheet with id= A, first strand: chain 'A' and resid 59 through 63 removed outlier: 6.814A pdb=" N LEU A 248 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS A 62 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE A 250 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER A 311 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 251 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 313 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N SER A 253 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N CYS A 315 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 312 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 168 through 173 removed outlier: 6.454A pdb=" N VAL A 200 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 171 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 202 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A 173 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN A 204 " --> pdb=" O VAL A 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 59 through 63 removed outlier: 6.814A pdb=" N LEU B 248 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LYS B 62 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 250 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER B 311 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU B 251 " --> pdb=" O SER B 311 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 313 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER B 253 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS B 315 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL B 312 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 168 through 173 removed outlier: 6.455A pdb=" N VAL B 200 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL B 171 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE B 202 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL B 173 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN B 204 " --> pdb=" O VAL B 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 59 through 63 removed outlier: 6.813A pdb=" N LEU C 248 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS C 62 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 250 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER C 311 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N LEU C 251 " --> pdb=" O SER C 311 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 313 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER C 253 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS C 315 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 312 " --> pdb=" O PHE C 336 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 168 through 173 removed outlier: 6.457A pdb=" N VAL C 200 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N VAL C 171 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE C 202 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL C 173 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN C 204 " --> pdb=" O VAL C 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 59 through 63 removed outlier: 6.814A pdb=" N LEU D 248 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LYS D 62 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE D 250 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER D 311 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU D 251 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 313 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N SER D 253 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS D 315 " --> pdb=" O SER D 253 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL D 312 " --> pdb=" O PHE D 336 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 168 through 173 removed outlier: 6.460A pdb=" N VAL D 200 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL D 171 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE D 202 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 173 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASN D 204 " --> pdb=" O VAL D 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= H 279 hydrogen bonds defined for protein. 813 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: 2.18 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1437 1.31 - 1.43: 1980 1.43 - 1.55: 5011 1.55 - 1.68: 20 1.68 - 1.80: 124 Bond restraints: 8572 Sorted by residual: bond pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" OE2 RGP D 801 " pdb=" PA RGP D 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" OE2 RGP B 801 " pdb=" PA RGP B 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" OE2 RGP C 801 " pdb=" PA RGP C 801 " ideal model delta sigma weight residual 1.798 1.647 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CD RGP D 801 " pdb=" OE2 RGP D 801 " ideal model delta sigma weight residual 1.302 1.399 -0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 8567 not shown) Histogram of bond angle deviations from ideal: 98.39 - 106.02: 199 106.02 - 113.64: 5140 113.64 - 121.27: 4210 121.27 - 128.90: 1987 128.90 - 136.53: 48 Bond angle restraints: 11584 Sorted by residual: angle pdb=" O1B ADP A 802 " pdb=" PB ADP A 802 " pdb=" O3B ADP A 802 " ideal model delta sigma weight residual 119.90 107.28 12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1B ADP B 802 " pdb=" PB ADP B 802 " pdb=" O3B ADP B 802 " ideal model delta sigma weight residual 119.90 107.29 12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" O1B ADP D 802 " pdb=" PB ADP D 802 " pdb=" O2B ADP D 802 " ideal model delta sigma weight residual 119.90 107.32 12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" O1B ADP C 802 " pdb=" PB ADP C 802 " pdb=" O2B ADP C 802 " ideal model delta sigma weight residual 119.90 107.32 12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" OE2 RGP A 801 " pdb=" PA RGP A 801 " pdb=" OA3 RGP A 801 " ideal model delta sigma weight residual 97.78 109.45 -11.67 3.00e+00 1.11e-01 1.51e+01 ... (remaining 11579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.56: 5060 31.56 - 63.11: 176 63.11 - 94.67: 6 94.67 - 126.22: 6 126.22 - 157.78: 4 Dihedral angle restraints: 5252 sinusoidal: 2130 harmonic: 3122 Sorted by residual: dihedral pdb=" O1B ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " pdb=" PA ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 97.77 -157.78 1 2.00e+01 2.50e-03 4.62e+01 dihedral pdb=" O1B ADP B 802 " pdb=" O3A ADP B 802 " pdb=" PB ADP B 802 " pdb=" PA ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 97.34 -157.35 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PA ADP A 802 " pdb=" PB ADP A 802 " ideal model delta sinusoidal sigma weight residual -60.00 70.54 -130.54 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 547 0.029 - 0.057: 508 0.057 - 0.086: 211 0.086 - 0.114: 92 0.114 - 0.143: 15 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE A 199 " pdb=" N ILE A 199 " pdb=" C ILE A 199 " pdb=" CB ILE A 199 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1370 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 175 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.40e+00 pdb=" N PRO A 176 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 175 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO D 176 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 176 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 176 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 175 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO C 176 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 176 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 176 " -0.021 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 291 2.70 - 3.25: 8216 3.25 - 3.80: 12560 3.80 - 4.35: 16243 4.35 - 4.90: 28689 Nonbonded interactions: 65999 Sorted by model distance: nonbonded pdb=" O THR D 275 " pdb=" OG SER D 279 " model vdw 2.150 2.440 nonbonded pdb=" OA3 RGP A 801 " pdb="MG MG A 803 " model vdw 2.152 2.170 nonbonded pdb=" OA3 RGP D 801 " pdb="MG MG D 803 " model vdw 2.154 2.170 nonbonded pdb=" OA3 RGP B 801 " pdb="MG MG B 803 " model vdw 2.166 2.170 nonbonded pdb=" OA3 RGP C 801 " pdb="MG MG C 803 " model vdw 2.171 2.170 ... (remaining 65994 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' and (resid 45 through 276 or resid 295 through 338 or resid 801 throu \ gh 803)) selection = (chain 'C' and (resid 45 through 276 or resid 295 through 338 or resid 801 throu \ gh 803)) selection = (chain 'D' and (resid 45 through 276 or resid 295 through 338 or resid 801 throu \ gh 803)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 5.880 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.120 Find NCS groups from input model: 0.600 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.011 0.151 8572 Z= 0.718 Angle : 0.914 12.622 11584 Z= 0.425 Chirality : 0.048 0.143 1373 Planarity : 0.004 0.039 1447 Dihedral : 16.740 157.776 3216 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.70 % Allowed : 16.99 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.51 (0.23), residues: 1042 helix: -1.50 (0.21), residues: 526 sheet: -3.17 (0.31), residues: 156 loop : -2.96 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 264 HIS 0.004 0.001 HIS D 92 PHE 0.010 0.002 PHE A 335 TYR 0.014 0.002 TYR A 274 ARG 0.002 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8867 (mttt) cc_final: 0.8645 (mtmm) REVERT: A 57 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7573 (mmp-170) REVERT: A 94 GLU cc_start: 0.8240 (tt0) cc_final: 0.7637 (tm-30) REVERT: A 118 LEU cc_start: 0.7847 (tp) cc_final: 0.7605 (tp) REVERT: A 247 ASP cc_start: 0.8065 (m-30) cc_final: 0.7434 (m-30) REVERT: A 274 TYR cc_start: 0.8453 (t80) cc_final: 0.8199 (t80) REVERT: B 57 ARG cc_start: 0.7871 (tpt170) cc_final: 0.7597 (mmp-170) REVERT: B 94 GLU cc_start: 0.8214 (tt0) cc_final: 0.7641 (tm-30) REVERT: B 118 LEU cc_start: 0.7849 (tp) cc_final: 0.7607 (tp) REVERT: B 245 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8165 (mm-40) REVERT: B 247 ASP cc_start: 0.8067 (m-30) cc_final: 0.7449 (m-30) REVERT: B 274 TYR cc_start: 0.8112 (t80) cc_final: 0.7738 (t80) REVERT: C 57 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7606 (mmp-170) REVERT: C 94 GLU cc_start: 0.8244 (tt0) cc_final: 0.7636 (tm-30) REVERT: C 118 LEU cc_start: 0.7850 (tp) cc_final: 0.7616 (tp) REVERT: C 247 ASP cc_start: 0.8067 (m-30) cc_final: 0.7425 (m-30) REVERT: C 274 TYR cc_start: 0.8107 (t80) cc_final: 0.7728 (t80) REVERT: D 57 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7558 (mmp-170) REVERT: D 94 GLU cc_start: 0.8247 (tt0) cc_final: 0.7630 (tm-30) REVERT: D 118 LEU cc_start: 0.7852 (tp) cc_final: 0.7616 (tp) REVERT: D 247 ASP cc_start: 0.8052 (m-30) cc_final: 0.7415 (m-30) REVERT: D 274 TYR cc_start: 0.8057 (t80) cc_final: 0.7681 (t80) outliers start: 34 outliers final: 27 residues processed: 206 average time/residue: 0.2011 time to fit residues: 56.9075 Evaluate side-chains 184 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 256 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 126 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 272 HIS B 170 GLN B 272 HIS C 52 GLN C 170 GLN C 272 HIS D 52 GLN D 170 GLN D 272 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8572 Z= 0.199 Angle : 0.551 6.442 11584 Z= 0.248 Chirality : 0.041 0.127 1373 Planarity : 0.003 0.029 1447 Dihedral : 11.755 130.978 1244 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.74 % Allowed : 21.46 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.25), residues: 1042 helix: -0.51 (0.23), residues: 547 sheet: -2.69 (0.34), residues: 156 loop : -2.25 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 264 HIS 0.001 0.001 HIS C 92 PHE 0.007 0.001 PHE A 335 TYR 0.005 0.001 TYR D 274 ARG 0.001 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8378 (mt0) cc_final: 0.8086 (mt0) REVERT: A 57 ARG cc_start: 0.7763 (tpt170) cc_final: 0.7547 (mmp-170) REVERT: A 94 GLU cc_start: 0.8249 (tt0) cc_final: 0.7554 (tm-30) REVERT: A 177 ASP cc_start: 0.7657 (m-30) cc_final: 0.6874 (t0) REVERT: A 247 ASP cc_start: 0.8123 (m-30) cc_final: 0.7486 (m-30) REVERT: B 52 GLN cc_start: 0.8419 (mt0) cc_final: 0.8136 (mt0) REVERT: B 57 ARG cc_start: 0.7807 (tpt170) cc_final: 0.7586 (mmp-170) REVERT: B 94 GLU cc_start: 0.8242 (tt0) cc_final: 0.7552 (tm-30) REVERT: B 177 ASP cc_start: 0.7661 (m-30) cc_final: 0.6872 (t0) REVERT: B 247 ASP cc_start: 0.8124 (m-30) cc_final: 0.7482 (m-30) REVERT: C 57 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7592 (mmp-170) REVERT: C 94 GLU cc_start: 0.8257 (tt0) cc_final: 0.7551 (tm-30) REVERT: C 118 LEU cc_start: 0.7689 (tp) cc_final: 0.7488 (tp) REVERT: C 177 ASP cc_start: 0.7659 (m-30) cc_final: 0.6880 (t0) REVERT: C 247 ASP cc_start: 0.8123 (m-30) cc_final: 0.7480 (m-30) REVERT: D 57 ARG cc_start: 0.7812 (tpt170) cc_final: 0.7569 (mmp-170) REVERT: D 94 GLU cc_start: 0.8259 (tt0) cc_final: 0.7547 (tm-30) REVERT: D 177 ASP cc_start: 0.7647 (m-30) cc_final: 0.6862 (t0) REVERT: D 247 ASP cc_start: 0.8110 (m-30) cc_final: 0.7465 (m-30) outliers start: 16 outliers final: 11 residues processed: 197 average time/residue: 0.2134 time to fit residues: 56.8029 Evaluate side-chains 185 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 310 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 0.0170 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8572 Z= 0.212 Angle : 0.548 6.338 11584 Z= 0.245 Chirality : 0.041 0.131 1373 Planarity : 0.003 0.029 1447 Dihedral : 10.731 131.514 1214 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.29 % Allowed : 22.11 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.26), residues: 1042 helix: -0.09 (0.23), residues: 546 sheet: -2.47 (0.35), residues: 156 loop : -1.83 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 304 HIS 0.001 0.001 HIS D 92 PHE 0.016 0.002 PHE A 188 TYR 0.022 0.001 TYR C 274 ARG 0.001 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8312 (mt0) cc_final: 0.8086 (mt0) REVERT: A 57 ARG cc_start: 0.7807 (tpt170) cc_final: 0.7581 (mmp-170) REVERT: A 94 GLU cc_start: 0.8246 (tt0) cc_final: 0.7581 (tm-30) REVERT: A 177 ASP cc_start: 0.7726 (m-30) cc_final: 0.6844 (t0) REVERT: A 247 ASP cc_start: 0.8157 (m-30) cc_final: 0.7530 (m-30) REVERT: B 52 GLN cc_start: 0.8350 (mt0) cc_final: 0.8143 (mt0) REVERT: B 57 ARG cc_start: 0.7812 (tpt170) cc_final: 0.7577 (mmp-170) REVERT: B 94 GLU cc_start: 0.8192 (tt0) cc_final: 0.7540 (tm-30) REVERT: B 177 ASP cc_start: 0.7703 (m-30) cc_final: 0.6823 (t0) REVERT: B 247 ASP cc_start: 0.8132 (m-30) cc_final: 0.7487 (m-30) REVERT: C 57 ARG cc_start: 0.7840 (tpt170) cc_final: 0.7575 (mmp-170) REVERT: C 94 GLU cc_start: 0.8249 (tt0) cc_final: 0.7579 (tm-30) REVERT: C 177 ASP cc_start: 0.7742 (m-30) cc_final: 0.6933 (t0) REVERT: C 247 ASP cc_start: 0.8136 (m-30) cc_final: 0.7490 (m-30) REVERT: C 261 LYS cc_start: 0.5471 (OUTLIER) cc_final: 0.5265 (mttt) REVERT: D 57 ARG cc_start: 0.7821 (tpt170) cc_final: 0.7562 (mmp-170) REVERT: D 94 GLU cc_start: 0.8248 (tt0) cc_final: 0.7571 (tm-30) REVERT: D 177 ASP cc_start: 0.7718 (m-30) cc_final: 0.6833 (t0) REVERT: D 247 ASP cc_start: 0.8148 (m-30) cc_final: 0.7505 (m-30) outliers start: 21 outliers final: 5 residues processed: 201 average time/residue: 0.2107 time to fit residues: 57.6915 Evaluate side-chains 190 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 198 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 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 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8572 Z= 0.208 Angle : 0.554 6.391 11584 Z= 0.248 Chirality : 0.041 0.129 1373 Planarity : 0.003 0.031 1447 Dihedral : 10.079 127.112 1210 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.05 % Allowed : 21.35 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 1042 helix: 0.09 (0.24), residues: 546 sheet: -2.23 (0.36), residues: 156 loop : -1.52 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 304 HIS 0.001 0.001 HIS D 92 PHE 0.017 0.002 PHE B 188 TYR 0.023 0.001 TYR B 274 ARG 0.001 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7737 (tp30) cc_final: 0.7206 (pt0) REVERT: A 52 GLN cc_start: 0.8371 (mt0) cc_final: 0.8079 (mt0) REVERT: A 57 ARG cc_start: 0.7766 (tpt170) cc_final: 0.7530 (mmp-170) REVERT: A 94 GLU cc_start: 0.8245 (tt0) cc_final: 0.7568 (tm-30) REVERT: A 177 ASP cc_start: 0.7719 (m-30) cc_final: 0.6869 (t0) REVERT: A 247 ASP cc_start: 0.8161 (m-30) cc_final: 0.7531 (m-30) REVERT: B 57 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7570 (mmp-170) REVERT: B 94 GLU cc_start: 0.8242 (tt0) cc_final: 0.7565 (tm-30) REVERT: B 177 ASP cc_start: 0.7728 (m-30) cc_final: 0.6841 (t0) REVERT: B 247 ASP cc_start: 0.8161 (m-30) cc_final: 0.7528 (m-30) REVERT: C 57 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7524 (mmp-170) REVERT: C 94 GLU cc_start: 0.8247 (tt0) cc_final: 0.7560 (tm-30) REVERT: C 177 ASP cc_start: 0.7746 (m-30) cc_final: 0.6954 (t0) REVERT: C 247 ASP cc_start: 0.8162 (m-30) cc_final: 0.7530 (m-30) REVERT: C 261 LYS cc_start: 0.5260 (OUTLIER) cc_final: 0.4797 (tptt) REVERT: D 57 ARG cc_start: 0.7816 (tpt170) cc_final: 0.7556 (mmp-170) REVERT: D 94 GLU cc_start: 0.8246 (tt0) cc_final: 0.7556 (tm-30) REVERT: D 177 ASP cc_start: 0.7711 (m-30) cc_final: 0.6856 (t0) REVERT: D 247 ASP cc_start: 0.8153 (m-30) cc_final: 0.7523 (m-30) outliers start: 28 outliers final: 20 residues processed: 206 average time/residue: 0.1995 time to fit residues: 56.1920 Evaluate side-chains 203 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.0370 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8572 Z= 0.181 Angle : 0.537 6.131 11584 Z= 0.240 Chirality : 0.041 0.128 1373 Planarity : 0.003 0.031 1447 Dihedral : 9.355 125.729 1210 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.27 % Allowed : 21.57 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 1042 helix: 0.23 (0.24), residues: 549 sheet: -1.90 (0.37), residues: 156 loop : -1.27 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 304 HIS 0.002 0.001 HIS C 74 PHE 0.020 0.001 PHE A 188 TYR 0.019 0.001 TYR B 274 ARG 0.001 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8363 (mt0) cc_final: 0.8085 (mt0) REVERT: A 57 ARG cc_start: 0.7771 (tpt170) cc_final: 0.7535 (mmp-170) REVERT: A 94 GLU cc_start: 0.8249 (tt0) cc_final: 0.7568 (tm-30) REVERT: A 177 ASP cc_start: 0.7725 (m-30) cc_final: 0.6886 (t0) REVERT: A 247 ASP cc_start: 0.8174 (m-30) cc_final: 0.7530 (m-30) REVERT: B 57 ARG cc_start: 0.7777 (tpt170) cc_final: 0.7529 (mmp-170) REVERT: B 94 GLU cc_start: 0.8244 (tt0) cc_final: 0.7569 (tm-30) REVERT: B 177 ASP cc_start: 0.7722 (m-30) cc_final: 0.6857 (t0) REVERT: B 247 ASP cc_start: 0.8177 (m-30) cc_final: 0.7540 (m-30) REVERT: C 57 ARG cc_start: 0.7798 (tpt170) cc_final: 0.7524 (mmp-170) REVERT: C 94 GLU cc_start: 0.8268 (tt0) cc_final: 0.7584 (tm-30) REVERT: C 177 ASP cc_start: 0.7743 (m-30) cc_final: 0.6892 (t0) REVERT: C 247 ASP cc_start: 0.8176 (m-30) cc_final: 0.7537 (m-30) REVERT: C 261 LYS cc_start: 0.5311 (OUTLIER) cc_final: 0.4900 (ttmt) REVERT: D 57 ARG cc_start: 0.7788 (tpt170) cc_final: 0.7519 (mmp-170) REVERT: D 94 GLU cc_start: 0.8238 (tt0) cc_final: 0.7530 (tm-30) REVERT: D 177 ASP cc_start: 0.7710 (m-30) cc_final: 0.6876 (t0) REVERT: D 247 ASP cc_start: 0.8168 (m-30) cc_final: 0.7535 (m-30) outliers start: 30 outliers final: 24 residues processed: 208 average time/residue: 0.2055 time to fit residues: 58.5731 Evaluate side-chains 207 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 8572 Z= 0.284 Angle : 0.576 6.034 11584 Z= 0.262 Chirality : 0.042 0.132 1373 Planarity : 0.003 0.030 1447 Dihedral : 9.348 130.358 1210 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.47 % Allowed : 21.02 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.27), residues: 1042 helix: 0.16 (0.23), residues: 546 sheet: -1.72 (0.40), residues: 156 loop : -1.17 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 304 HIS 0.002 0.000 HIS D 92 PHE 0.011 0.002 PHE B 188 TYR 0.019 0.002 TYR B 274 ARG 0.001 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7787 (tpt170) cc_final: 0.7536 (mmp-170) REVERT: A 94 GLU cc_start: 0.8222 (tt0) cc_final: 0.7548 (tm-30) REVERT: A 177 ASP cc_start: 0.7769 (m-30) cc_final: 0.6934 (t0) REVERT: A 247 ASP cc_start: 0.8205 (m-30) cc_final: 0.7599 (m-30) REVERT: B 57 ARG cc_start: 0.7798 (tpt170) cc_final: 0.7540 (mmp-170) REVERT: B 94 GLU cc_start: 0.8220 (tt0) cc_final: 0.7552 (tm-30) REVERT: B 177 ASP cc_start: 0.7763 (m-30) cc_final: 0.6886 (t0) REVERT: B 247 ASP cc_start: 0.8166 (m-30) cc_final: 0.7544 (m-30) REVERT: C 57 ARG cc_start: 0.7807 (tpt170) cc_final: 0.7529 (mmp-170) REVERT: C 94 GLU cc_start: 0.8235 (tt0) cc_final: 0.7533 (tm-30) REVERT: C 177 ASP cc_start: 0.7787 (m-30) cc_final: 0.6936 (t0) REVERT: C 247 ASP cc_start: 0.8199 (m-30) cc_final: 0.7580 (m-30) REVERT: C 261 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.4839 (ttmt) REVERT: D 57 ARG cc_start: 0.7800 (tpt170) cc_final: 0.7527 (mmp-170) REVERT: D 94 GLU cc_start: 0.8224 (tt0) cc_final: 0.7552 (tm-30) REVERT: D 177 ASP cc_start: 0.7756 (m-30) cc_final: 0.6891 (t0) REVERT: D 247 ASP cc_start: 0.8153 (m-30) cc_final: 0.7532 (m-30) outliers start: 41 outliers final: 27 residues processed: 214 average time/residue: 0.2035 time to fit residues: 59.6182 Evaluate side-chains 209 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8572 Z= 0.229 Angle : 0.565 6.240 11584 Z= 0.254 Chirality : 0.041 0.131 1373 Planarity : 0.003 0.030 1447 Dihedral : 9.144 129.921 1210 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.81 % Allowed : 21.02 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.27), residues: 1042 helix: 0.32 (0.24), residues: 546 sheet: -1.64 (0.40), residues: 156 loop : -1.07 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 264 HIS 0.001 0.000 HIS D 92 PHE 0.018 0.001 PHE C 188 TYR 0.019 0.001 TYR B 274 ARG 0.001 0.000 ARG B 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7791 (tpt170) cc_final: 0.7543 (mmp-170) REVERT: A 94 GLU cc_start: 0.8217 (tt0) cc_final: 0.7558 (tm-30) REVERT: A 177 ASP cc_start: 0.7761 (m-30) cc_final: 0.6909 (t0) REVERT: B 57 ARG cc_start: 0.7814 (tpt170) cc_final: 0.7588 (mmp-170) REVERT: B 94 GLU cc_start: 0.8221 (tt0) cc_final: 0.7558 (tm-30) REVERT: B 177 ASP cc_start: 0.7754 (m-30) cc_final: 0.6892 (t0) REVERT: C 57 ARG cc_start: 0.7819 (tpt170) cc_final: 0.7537 (mmp-170) REVERT: C 94 GLU cc_start: 0.8225 (tt0) cc_final: 0.7555 (tm-30) REVERT: C 177 ASP cc_start: 0.7775 (m-30) cc_final: 0.6937 (t0) REVERT: C 261 LYS cc_start: 0.5225 (OUTLIER) cc_final: 0.4885 (ttmt) REVERT: D 57 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7536 (mmp-170) REVERT: D 94 GLU cc_start: 0.8228 (tt0) cc_final: 0.7593 (tm-30) REVERT: D 177 ASP cc_start: 0.7748 (m-30) cc_final: 0.6914 (t0) outliers start: 35 outliers final: 29 residues processed: 205 average time/residue: 0.2061 time to fit residues: 57.8335 Evaluate side-chains 213 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8572 Z= 0.190 Angle : 0.548 6.710 11584 Z= 0.245 Chirality : 0.041 0.128 1373 Planarity : 0.003 0.030 1447 Dihedral : 8.807 127.094 1210 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.59 % Allowed : 21.57 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.64 (0.27), residues: 1042 helix: 0.52 (0.24), residues: 532 sheet: -1.55 (0.41), residues: 156 loop : -1.19 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 264 HIS 0.001 0.000 HIS D 92 PHE 0.023 0.001 PHE B 188 TYR 0.012 0.001 TYR A 274 ARG 0.001 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 181 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7799 (tpt170) cc_final: 0.7531 (mmp-170) REVERT: A 94 GLU cc_start: 0.8149 (tt0) cc_final: 0.7466 (tm-30) REVERT: A 177 ASP cc_start: 0.7751 (m-30) cc_final: 0.6936 (t0) REVERT: B 57 ARG cc_start: 0.7815 (tpt170) cc_final: 0.7537 (mmp-170) REVERT: B 94 GLU cc_start: 0.8176 (tt0) cc_final: 0.7552 (tm-30) REVERT: B 177 ASP cc_start: 0.7687 (m-30) cc_final: 0.6912 (t0) REVERT: C 57 ARG cc_start: 0.7809 (tpt170) cc_final: 0.7530 (mmp-170) REVERT: C 94 GLU cc_start: 0.8187 (tt0) cc_final: 0.7554 (tm-30) REVERT: C 177 ASP cc_start: 0.7702 (m-30) cc_final: 0.6960 (t0) REVERT: C 261 LYS cc_start: 0.5466 (OUTLIER) cc_final: 0.5198 (ttmt) REVERT: D 57 ARG cc_start: 0.7783 (tpt170) cc_final: 0.7565 (mmp-170) REVERT: D 94 GLU cc_start: 0.8174 (tt0) cc_final: 0.7537 (tm-30) REVERT: D 177 ASP cc_start: 0.7735 (m-30) cc_final: 0.6916 (t0) outliers start: 33 outliers final: 28 residues processed: 204 average time/residue: 0.2049 time to fit residues: 57.1435 Evaluate side-chains 208 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8572 Z= 0.194 Angle : 0.552 6.644 11584 Z= 0.248 Chirality : 0.041 0.128 1373 Planarity : 0.003 0.030 1447 Dihedral : 8.494 122.829 1210 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.27 % Allowed : 22.00 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.27), residues: 1042 helix: 0.62 (0.24), residues: 532 sheet: -1.44 (0.41), residues: 156 loop : -1.14 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 304 HIS 0.001 0.000 HIS D 92 PHE 0.013 0.001 PHE D 188 TYR 0.013 0.001 TYR C 274 ARG 0.001 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7789 (tpt170) cc_final: 0.7542 (mmp-170) REVERT: A 94 GLU cc_start: 0.8115 (tt0) cc_final: 0.7464 (tm-30) REVERT: A 177 ASP cc_start: 0.7758 (m-30) cc_final: 0.6942 (t0) REVERT: B 57 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7547 (mmp-170) REVERT: B 94 GLU cc_start: 0.8163 (tt0) cc_final: 0.7543 (tm-30) REVERT: B 177 ASP cc_start: 0.7690 (m-30) cc_final: 0.6918 (t0) REVERT: C 57 ARG cc_start: 0.7831 (tpt170) cc_final: 0.7549 (mmp-170) REVERT: C 94 GLU cc_start: 0.8121 (tt0) cc_final: 0.7455 (tm-30) REVERT: C 177 ASP cc_start: 0.7765 (m-30) cc_final: 0.6945 (t0) REVERT: C 261 LYS cc_start: 0.5451 (OUTLIER) cc_final: 0.5200 (ttmt) REVERT: D 94 GLU cc_start: 0.8121 (tt0) cc_final: 0.7448 (tm-30) REVERT: D 177 ASP cc_start: 0.7743 (m-30) cc_final: 0.6922 (t0) outliers start: 30 outliers final: 24 residues processed: 197 average time/residue: 0.2058 time to fit residues: 55.3991 Evaluate side-chains 202 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 ASN Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.0870 chunk 95 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8572 Z= 0.161 Angle : 0.545 7.227 11584 Z= 0.243 Chirality : 0.040 0.126 1373 Planarity : 0.003 0.031 1447 Dihedral : 8.150 118.298 1210 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.83 % Allowed : 22.66 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1042 helix: 0.76 (0.24), residues: 532 sheet: -1.32 (0.42), residues: 156 loop : -1.14 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 264 HIS 0.001 0.000 HIS D 92 PHE 0.012 0.001 PHE C 188 TYR 0.005 0.001 TYR D 55 ARG 0.001 0.000 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7533 (mmp-170) REVERT: A 94 GLU cc_start: 0.8136 (tt0) cc_final: 0.7420 (tm-30) REVERT: A 119 MET cc_start: 0.7680 (ttt) cc_final: 0.7417 (ttt) REVERT: A 177 ASP cc_start: 0.7681 (m-30) cc_final: 0.6959 (t0) REVERT: B 57 ARG cc_start: 0.7772 (tpt170) cc_final: 0.7538 (mmp-170) REVERT: B 94 GLU cc_start: 0.8111 (tt0) cc_final: 0.7452 (tm-30) REVERT: B 119 MET cc_start: 0.7725 (ttt) cc_final: 0.7452 (ttt) REVERT: B 177 ASP cc_start: 0.7675 (m-30) cc_final: 0.6918 (t0) REVERT: C 57 ARG cc_start: 0.7778 (tpt170) cc_final: 0.7524 (mmp-170) REVERT: C 94 GLU cc_start: 0.8126 (tt0) cc_final: 0.7432 (tm-30) REVERT: C 177 ASP cc_start: 0.7747 (m-30) cc_final: 0.6942 (t0) REVERT: C 252 MET cc_start: 0.8533 (mtp) cc_final: 0.7873 (mtp) REVERT: C 261 LYS cc_start: 0.5253 (OUTLIER) cc_final: 0.4934 (ttmt) REVERT: D 94 GLU cc_start: 0.8131 (tt0) cc_final: 0.7399 (tm-30) REVERT: D 177 ASP cc_start: 0.7660 (m-30) cc_final: 0.6941 (t0) outliers start: 26 outliers final: 18 residues processed: 199 average time/residue: 0.2052 time to fit residues: 55.9017 Evaluate side-chains 198 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 261 LYS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 127 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112657 restraints weight = 8541.285| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.65 r_work: 0.3171 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8572 Z= 0.261 Angle : 0.579 7.180 11584 Z= 0.262 Chirality : 0.042 0.131 1373 Planarity : 0.003 0.030 1447 Dihedral : 8.295 116.472 1210 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.18 % Allowed : 23.20 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.27), residues: 1042 helix: 0.62 (0.24), residues: 532 sheet: -1.31 (0.42), residues: 156 loop : -1.14 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 304 HIS 0.002 0.001 HIS D 92 PHE 0.015 0.001 PHE C 188 TYR 0.005 0.001 TYR D 259 ARG 0.001 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.48 seconds wall clock time: 37 minutes 24.31 seconds (2244.31 seconds total)