Starting phenix.real_space_refine (version: dev) on Mon Dec 12 01:20:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/12_2022/7wx3_32875_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/12_2022/7wx3_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_32875/12_2022/7wx3_32875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/12_2022/7wx3_32875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/12_2022/7wx3_32875_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wx3_32875/12_2022/7wx3_32875_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 5.31, per 1000 atoms: 0.63 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: 3.40 Conformation dependent library (CDL) restraints added in 1.2 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: 0.77 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: 2.22 Time building geometry restraints manager: 3.65 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 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. 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: 2.440 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: 6.180 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 25.690 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 % Cbeta Deviations : 0.39 % 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 *********************** 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 : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 27 residues processed: 206 average time/residue: 0.2058 time to fit residues: 58.4599 Evaluate side-chains 186 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0791 time to fit residues: 5.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.1353 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= 0.198 Angle : 0.563 6.186 11584 Z= 0.255 Chirality : 0.042 0.128 1373 Planarity : 0.003 0.029 1447 Dihedral : 11.763 130.964 1210 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.39 % 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: -2.29 (0.25), residues: 1042 helix: -0.55 (0.23), residues: 547 sheet: -2.75 (0.33), residues: 156 loop : -2.29 (0.30), residues: 339 *********************** 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 170 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 168 average time/residue: 0.2089 time to fit residues: 47.8755 Evaluate side-chains 169 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0777 time to fit residues: 2.1164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 8572 Z= 0.234 Angle : 0.573 6.368 11584 Z= 0.261 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.026 1447 Dihedral : 10.763 132.561 1210 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.39 % 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: -1.65 (0.26), residues: 1042 helix: -0.10 (0.23), residues: 546 sheet: -2.46 (0.35), residues: 156 loop : -1.85 (0.31), residues: 340 *********************** 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 208 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 199 average time/residue: 0.2128 time to fit residues: 57.9161 Evaluate side-chains 183 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1124 time to fit residues: 2.3004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.0980 chunk 71 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1936 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= 0.174 Angle : 0.548 6.423 11584 Z= 0.247 Chirality : 0.040 0.129 1373 Planarity : 0.003 0.030 1447 Dihedral : 10.131 127.758 1210 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.39 % 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: -1.16 (0.27), residues: 1042 helix: 0.18 (0.24), residues: 546 sheet: -2.06 (0.37), residues: 156 loop : -1.49 (0.32), residues: 340 *********************** 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 194 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 176 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 192 average time/residue: 0.2070 time to fit residues: 54.3376 Evaluate side-chains 176 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 172 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1563 time to fit residues: 2.2636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 8572 Z= 0.242 Angle : 0.569 6.251 11584 Z= 0.257 Chirality : 0.041 0.130 1373 Planarity : 0.003 0.028 1447 Dihedral : 9.644 126.778 1210 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.39 % 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: -1.08 (0.26), residues: 1042 helix: 0.17 (0.24), residues: 546 sheet: -1.76 (0.39), residues: 156 loop : -1.45 (0.32), residues: 340 *********************** 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 188 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 184 average time/residue: 0.2043 time to fit residues: 51.8514 Evaluate side-chains 175 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0787 time to fit residues: 2.7621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 8572 Z= 0.244 Angle : 0.567 5.991 11584 Z= 0.255 Chirality : 0.041 0.129 1373 Planarity : 0.003 0.028 1447 Dihedral : 9.384 130.298 1210 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.39 % 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: -0.93 (0.26), residues: 1042 helix: 0.27 (0.24), residues: 542 sheet: -1.66 (0.40), residues: 156 loop : -1.33 (0.31), residues: 344 *********************** 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 179 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 179 average time/residue: 0.2002 time to fit residues: 49.5102 Evaluate side-chains 173 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.0570 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.1980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 8572 Z= 0.158 Angle : 0.549 5.928 11584 Z= 0.246 Chirality : 0.040 0.125 1373 Planarity : 0.003 0.027 1447 Dihedral : 9.002 129.359 1210 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.39 % 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: -0.77 (0.26), residues: 1042 helix: 0.42 (0.24), residues: 549 sheet: -1.57 (0.40), residues: 156 loop : -1.34 (0.32), residues: 337 *********************** 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 176 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 175 average time/residue: 0.1902 time to fit residues: 46.7145 Evaluate side-chains 167 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0811 time to fit residues: 1.5026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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: 0.7726 moved from start: 0.2507 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= 0.167 Angle : 0.547 5.922 11584 Z= 0.245 Chirality : 0.040 0.126 1373 Planarity : 0.003 0.027 1447 Dihedral : 8.661 126.580 1210 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.39 % 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: 0.69 (0.24), residues: 528 sheet: -1.44 (0.41), residues: 156 loop : -1.25 (0.32), residues: 358 *********************** 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 167 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.1890 time to fit residues: 44.4076 Evaluate side-chains 163 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 8572 Z= 0.144 Angle : 0.545 5.952 11584 Z= 0.244 Chirality : 0.039 0.124 1373 Planarity : 0.003 0.027 1447 Dihedral : 8.303 122.599 1210 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.39 % 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: -0.19 (0.27), residues: 1042 helix: 0.94 (0.25), residues: 512 sheet: -1.26 (0.41), residues: 156 loop : -1.00 (0.32), residues: 374 *********************** 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 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1906 time to fit residues: 44.4996 Evaluate side-chains 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2686 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= 0.167 Angle : 0.548 5.990 11584 Z= 0.246 Chirality : 0.040 0.133 1373 Planarity : 0.003 0.027 1447 Dihedral : 8.161 119.584 1210 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.39 % 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: -0.28 (0.27), residues: 1042 helix: 0.90 (0.24), residues: 532 sheet: -1.14 (0.42), residues: 156 loop : -1.31 (0.32), residues: 354 ********************** 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 171 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 169 average time/residue: 0.1822 time to fit residues: 43.7859 Evaluate side-chains 168 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0880 time to fit residues: 1.6041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.155201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112184 restraints weight = 8615.659| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.67 r_work: 0.3157 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 8572 Z= 0.307 Angle : 0.616 7.646 11584 Z= 0.285 Chirality : 0.043 0.134 1373 Planarity : 0.003 0.026 1447 Dihedral : 8.492 119.101 1210 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.39 % 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: -0.44 (0.27), residues: 1042 helix: 0.72 (0.24), residues: 524 sheet: -1.11 (0.42), residues: 156 loop : -1.31 (0.31), residues: 362 =============================================================================== Job complete usr+sys time: 1873.20 seconds wall clock time: 34 minutes 39.61 seconds (2079.61 seconds total)