Starting phenix.real_space_refine (version: dev) on Wed Apr 6 21:49:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/04_2022/7s66_24851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/04_2022/7s66_24851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/04_2022/7s66_24851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/04_2022/7s66_24851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/04_2022/7s66_24851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/04_2022/7s66_24851_updated.pdb" } resolution = 2.8 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= 0.012 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 TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 193": "NH1" <-> "NH2" Residue "C PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 23242 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3807 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3807 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3811 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3811 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3811 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3811 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 472} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 13.33, per 1000 atoms: 0.57 Number of scatterers: 23242 At special positions: 0 Unit cell: (118.45, 118.45, 116.15, 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 90 16.00 P 36 15.00 Mg 12 11.99 O 4484 8.00 N 4080 7.00 C 14540 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 3.7 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 18 sheets defined 32.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 No H-bonds generated for 'chain 'A' and resid 28 through 31' Processing helix chain 'A' and resid 52 through 66 Processing helix chain 'A' and resid 80 through 90 removed outlier: 4.250A pdb=" N SER A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 123 through 136 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.512A pdb=" N PHE A 151 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 294 through 308 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 380 through 383 No H-bonds generated for 'chain 'A' and resid 380 through 383' Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'B' and resid 28 through 31 No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 52 through 66 Processing helix chain 'B' and resid 80 through 90 removed outlier: 4.250A pdb=" N SER B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 123 through 136 Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.512A pdb=" N PHE B 151 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 174 Processing helix chain 'B' and resid 197 through 200 No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'B' and resid 380 through 383 No H-bonds generated for 'chain 'B' and resid 380 through 383' Processing helix chain 'B' and resid 389 through 405 Processing helix chain 'C' and resid 28 through 31 No H-bonds generated for 'chain 'C' and resid 28 through 31' Processing helix chain 'C' and resid 52 through 66 Processing helix chain 'C' and resid 80 through 90 removed outlier: 4.251A pdb=" N SER C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 123 through 136 Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.513A pdb=" N PHE C 151 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLN C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 174 Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 294 through 308 Processing helix chain 'C' and resid 321 through 331 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 356 through 370 Processing helix chain 'C' and resid 380 through 383 No H-bonds generated for 'chain 'C' and resid 380 through 383' Processing helix chain 'C' and resid 389 through 405 Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 52 through 66 Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.251A pdb=" N SER D 89 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE D 90 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.512A pdb=" N PHE D 151 " --> pdb=" O THR D 148 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN D 152 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 174 Processing helix chain 'D' and resid 197 through 200 No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 268 through 273 Processing helix chain 'D' and resid 294 through 308 Processing helix chain 'D' and resid 321 through 331 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 356 through 370 Processing helix chain 'D' and resid 380 through 383 No H-bonds generated for 'chain 'D' and resid 380 through 383' Processing helix chain 'D' and resid 389 through 405 Processing helix chain 'E' and resid 28 through 31 No H-bonds generated for 'chain 'E' and resid 28 through 31' Processing helix chain 'E' and resid 52 through 66 Processing helix chain 'E' and resid 80 through 90 removed outlier: 4.250A pdb=" N SER E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 123 through 136 Processing helix chain 'E' and resid 147 through 153 removed outlier: 3.512A pdb=" N PHE E 151 " --> pdb=" O THR E 148 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 174 Processing helix chain 'E' and resid 197 through 200 No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 268 through 273 Processing helix chain 'E' and resid 294 through 308 Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 335 through 340 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 356 through 370 Processing helix chain 'E' and resid 380 through 383 No H-bonds generated for 'chain 'E' and resid 380 through 383' Processing helix chain 'E' and resid 389 through 405 Processing helix chain 'F' and resid 28 through 31 No H-bonds generated for 'chain 'F' and resid 28 through 31' Processing helix chain 'F' and resid 52 through 66 Processing helix chain 'F' and resid 80 through 90 removed outlier: 4.251A pdb=" N SER F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 123 through 136 Processing helix chain 'F' and resid 147 through 153 removed outlier: 3.513A pdb=" N PHE F 151 " --> pdb=" O THR F 148 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN F 152 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 174 Processing helix chain 'F' and resid 197 through 200 No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 268 through 273 Processing helix chain 'F' and resid 294 through 308 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 351 through 353 No H-bonds generated for 'chain 'F' and resid 351 through 353' Processing helix chain 'F' and resid 356 through 370 Processing helix chain 'F' and resid 380 through 383 No H-bonds generated for 'chain 'F' and resid 380 through 383' Processing helix chain 'F' and resid 389 through 405 Processing sheet with id= A, first strand: chain 'A' and resid 234 through 236 removed outlier: 6.631A pdb=" N VAL A 204 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 203 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 178 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 44 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET A 180 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY A 46 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 240 Processing sheet with id= C, first strand: chain 'A' and resid 476 through 479 removed outlier: 4.159A pdb=" N ARG A 451 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE A 472 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 12.711A pdb=" N MET A 449 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 437 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY A 410 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA A 286 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 412 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY A 288 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN A 414 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 234 through 236 removed outlier: 6.630A pdb=" N VAL B 204 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 203 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 178 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 44 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET B 180 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY B 46 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 237 through 240 Processing sheet with id= F, first strand: chain 'B' and resid 476 through 479 removed outlier: 4.160A pdb=" N ARG B 451 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE B 472 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 12.711A pdb=" N MET B 449 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 437 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY B 410 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA B 286 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE B 412 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY B 288 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN B 414 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 234 through 236 removed outlier: 6.631A pdb=" N VAL C 204 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 203 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR C 178 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL C 44 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET C 180 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY C 46 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 237 through 240 Processing sheet with id= I, first strand: chain 'C' and resid 476 through 479 removed outlier: 4.159A pdb=" N ARG C 451 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE C 472 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 12.710A pdb=" N MET C 449 " --> pdb=" O ILE C 472 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 437 " --> pdb=" O PHE C 456 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY C 410 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA C 286 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE C 412 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY C 288 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN C 414 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 234 through 236 removed outlier: 6.631A pdb=" N VAL D 204 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN D 203 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR D 178 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL D 44 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET D 180 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY D 46 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 237 through 240 Processing sheet with id= L, first strand: chain 'D' and resid 476 through 479 removed outlier: 4.159A pdb=" N ARG D 451 " --> pdb=" O PHE D 470 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE D 472 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N MET D 449 " --> pdb=" O ILE D 472 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE D 437 " --> pdb=" O PHE D 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY D 410 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA D 286 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE D 412 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY D 288 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN D 414 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 234 through 236 removed outlier: 6.631A pdb=" N VAL E 204 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN E 203 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR E 178 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL E 44 " --> pdb=" O THR E 178 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET E 180 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY E 46 " --> pdb=" O MET E 180 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 237 through 240 Processing sheet with id= O, first strand: chain 'E' and resid 476 through 479 removed outlier: 4.159A pdb=" N ARG E 451 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ILE E 472 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N MET E 449 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE E 437 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY E 410 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA E 286 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE E 412 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY E 288 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN E 414 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 234 through 236 removed outlier: 6.632A pdb=" N VAL F 204 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN F 203 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR F 178 " --> pdb=" O THR F 42 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL F 44 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET F 180 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N GLY F 46 " --> pdb=" O MET F 180 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 237 through 240 Processing sheet with id= R, first strand: chain 'F' and resid 476 through 479 removed outlier: 4.160A pdb=" N ARG F 451 " --> pdb=" O PHE F 470 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N ILE F 472 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 12.712A pdb=" N MET F 449 " --> pdb=" O ILE F 472 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 437 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY F 410 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ALA F 286 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE F 412 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY F 288 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASN F 414 " --> pdb=" O GLY F 288 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2592 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: 7.61 Time building geometry restraints manager: 10.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4799 1.32 - 1.45: 5403 1.45 - 1.57: 13220 1.57 - 1.69: 60 1.69 - 1.81: 162 Bond restraints: 23644 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP F 901 " pdb=" C5 ATP F 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C4 ATP C 901 " pdb=" C5 ATP C 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 901 " pdb=" C5 ATP B 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 ... (remaining 23639 not shown) Histogram of bond angle deviations from ideal: 99.74 - 107.05: 614 107.05 - 114.36: 13317 114.36 - 121.66: 12827 121.66 - 128.97: 5092 128.97 - 136.28: 108 Bond angle restraints: 31958 Sorted by residual: angle pdb=" PB ATP C 901 " pdb=" O3B ATP C 901 " pdb=" PG ATP C 901 " ideal model delta sigma weight residual 139.87 117.82 22.05 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 117.86 22.01 1.00e+00 1.00e+00 4.84e+02 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 117.86 22.01 1.00e+00 1.00e+00 4.84e+02 angle pdb=" PB ATP F 901 " pdb=" O3B ATP F 901 " pdb=" PG ATP F 901 " ideal model delta sigma weight residual 139.87 117.88 21.99 1.00e+00 1.00e+00 4.84e+02 angle pdb=" PB ATP B 901 " pdb=" O3B ATP B 901 " pdb=" PG ATP B 901 " ideal model delta sigma weight residual 139.87 117.88 21.99 1.00e+00 1.00e+00 4.84e+02 ... (remaining 31953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 13448 17.48 - 34.97: 442 34.97 - 52.45: 96 52.45 - 69.93: 36 69.93 - 87.41: 12 Dihedral angle restraints: 14034 sinusoidal: 5718 harmonic: 8316 Sorted by residual: dihedral pdb=" CA TYR F 154 " pdb=" C TYR F 154 " pdb=" N ASP F 155 " pdb=" CA ASP F 155 " ideal model delta harmonic sigma weight residual -180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR A 154 " pdb=" C TYR A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -159.97 -20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA TYR E 154 " pdb=" C TYR E 154 " pdb=" N ASP E 155 " pdb=" CA ASP E 155 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 14031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2015 0.048 - 0.095: 1082 0.095 - 0.143: 364 0.143 - 0.191: 73 0.191 - 0.238: 24 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CA TRP E 92 " pdb=" N TRP E 92 " pdb=" C TRP E 92 " pdb=" CB TRP E 92 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA TRP F 92 " pdb=" N TRP F 92 " pdb=" C TRP F 92 " pdb=" CB TRP F 92 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA TRP C 92 " pdb=" N TRP C 92 " pdb=" C TRP C 92 " pdb=" CB TRP C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3555 not shown) Planarity restraints: 4090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 92 " -0.083 2.00e-02 2.50e+03 4.15e-02 4.30e+01 pdb=" CG TRP B 92 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 92 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 92 " 0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP B 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 92 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 92 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 92 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 92 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 92 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 92 " 0.083 2.00e-02 2.50e+03 4.15e-02 4.30e+01 pdb=" CG TRP C 92 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP C 92 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 92 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP C 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP C 92 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP C 92 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 92 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 92 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 92 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 92 " -0.082 2.00e-02 2.50e+03 4.14e-02 4.28e+01 pdb=" CG TRP A 92 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 92 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 92 " 0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP A 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 92 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 92 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 92 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 92 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 92 " -0.037 2.00e-02 2.50e+03 ... (remaining 4087 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 42 2.40 - 3.02: 13811 3.02 - 3.65: 33997 3.65 - 4.27: 56766 4.27 - 4.90: 93177 Nonbonded interactions: 197793 Sorted by model distance: nonbonded pdb=" OG1 THR F 53 " pdb="MG MG F 904 " model vdw 1.770 2.170 nonbonded pdb=" OG1 THR D 53 " pdb="MG MG D 904 " model vdw 1.770 2.170 nonbonded pdb=" OG1 THR E 53 " pdb="MG MG E 904 " model vdw 1.771 2.170 nonbonded pdb=" OG1 THR A 53 " pdb="MG MG A 904 " model vdw 1.771 2.170 nonbonded pdb=" OG1 THR C 53 " pdb="MG MG C 904 " model vdw 1.771 2.170 ... (remaining 197788 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 14 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 through 498 or resid 901 through 904)) selection = (chain 'D' and (resid 14 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 through 498 or resid 901 through 904)) selection = (chain 'E' and (resid 14 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 through 498 or resid 901 through 904)) selection = (chain 'F' and (resid 14 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )) or resid 114 through 498 or resid 901 through 904)) } 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 36 5.49 5 Mg 12 5.21 5 S 90 5.16 5 C 14540 2.51 5 N 4080 2.21 5 O 4484 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: 0.610 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: 4.000 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.190 Process input model: 59.730 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.013 0.080 23644 Z= 0.859 Angle : 1.344 22.048 31958 Z= 1.009 Chirality : 0.063 0.238 3558 Planarity : 0.010 0.042 4090 Dihedral : 10.544 87.414 8694 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 0.00 % 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: 0.50 (0.15), residues: 2898 helix: 0.06 (0.14), residues: 1038 sheet: 0.80 (0.20), residues: 774 loop : 0.53 (0.19), residues: 1086 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 2.811 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 1.6232 time to fit residues: 1114.8849 Evaluate side-chains 313 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 2.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.6980 chunk 218 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 23644 Z= 0.170 Angle : 0.492 5.813 31958 Z= 0.275 Chirality : 0.042 0.135 3558 Planarity : 0.003 0.028 4090 Dihedral : 5.577 65.717 3240 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer Outliers : 2.90 % 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: 1.11 (0.16), residues: 2898 helix: 1.34 (0.16), residues: 1044 sheet: 0.61 (0.19), residues: 780 loop : 0.42 (0.19), residues: 1074 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 337 time to evaluate : 3.020 Fit side-chains outliers start: 71 outliers final: 17 residues processed: 393 average time/residue: 1.3436 time to fit residues: 604.6964 Evaluate side-chains 301 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 284 time to evaluate : 2.626 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.2372 time to fit residues: 3.9994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.0570 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 0.0370 chunk 178 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 overall best weight: 2.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 GLN F 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 23644 Z= 0.270 Angle : 0.498 6.100 31958 Z= 0.271 Chirality : 0.044 0.182 3558 Planarity : 0.004 0.029 4090 Dihedral : 6.064 89.138 3240 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 3.31 % 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: 1.07 (0.16), residues: 2898 helix: 1.72 (0.16), residues: 1008 sheet: 0.26 (0.18), residues: 780 loop : 0.25 (0.19), residues: 1110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 321 time to evaluate : 2.999 Fit side-chains outliers start: 81 outliers final: 43 residues processed: 393 average time/residue: 1.4613 time to fit residues: 653.5516 Evaluate side-chains 313 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 270 time to evaluate : 3.044 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 1.0014 time to fit residues: 8.3352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 249 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 341 GLN E 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 23644 Z= 0.209 Angle : 0.445 5.962 31958 Z= 0.242 Chirality : 0.042 0.161 3558 Planarity : 0.003 0.042 4090 Dihedral : 5.866 89.772 3240 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 3.27 % 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: 1.07 (0.16), residues: 2898 helix: 1.81 (0.16), residues: 1008 sheet: 0.23 (0.18), residues: 786 loop : 0.19 (0.19), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 297 time to evaluate : 2.860 Fit side-chains revert: symmetry clash outliers start: 80 outliers final: 46 residues processed: 366 average time/residue: 1.4144 time to fit residues: 589.2922 Evaluate side-chains 310 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 2.912 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 44 residues processed: 2 average time/residue: 0.2221 time to fit residues: 4.5288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 249 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 361 GLN B 368 ASN C 361 GLN D 368 ASN E 368 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 23644 Z= 0.397 Angle : 0.542 6.234 31958 Z= 0.289 Chirality : 0.046 0.243 3558 Planarity : 0.004 0.029 4090 Dihedral : 5.942 83.351 3240 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 3.97 % 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: 0.54 (0.15), residues: 2898 helix: 1.39 (0.16), residues: 1038 sheet: 0.01 (0.18), residues: 756 loop : -0.25 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 288 time to evaluate : 3.163 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 57 residues processed: 361 average time/residue: 1.5132 time to fit residues: 620.1350 Evaluate side-chains 315 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 258 time to evaluate : 2.912 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 51 residues processed: 7 average time/residue: 0.3850 time to fit residues: 7.9083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 163 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN C 361 GLN F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 23644 Z= 0.289 Angle : 0.477 5.950 31958 Z= 0.256 Chirality : 0.043 0.213 3558 Planarity : 0.003 0.040 4090 Dihedral : 5.763 79.301 3240 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 3.39 % 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: 0.56 (0.15), residues: 2898 helix: 1.47 (0.16), residues: 1038 sheet: 0.01 (0.18), residues: 756 loop : -0.30 (0.17), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 283 time to evaluate : 3.205 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 48 residues processed: 350 average time/residue: 1.5079 time to fit residues: 599.1742 Evaluate side-chains 312 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 264 time to evaluate : 3.048 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 45 residues processed: 3 average time/residue: 0.5496 time to fit residues: 6.4012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN F 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 23644 Z= 0.277 Angle : 0.479 5.722 31958 Z= 0.257 Chirality : 0.043 0.187 3558 Planarity : 0.004 0.047 4090 Dihedral : 5.717 78.190 3240 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 3.39 % 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: 0.60 (0.15), residues: 2898 helix: 1.51 (0.16), residues: 1038 sheet: -0.03 (0.18), residues: 780 loop : -0.24 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 283 time to evaluate : 2.907 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 55 residues processed: 349 average time/residue: 1.4356 time to fit residues: 572.2750 Evaluate side-chains 318 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 263 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 51 residues processed: 6 average time/residue: 0.7333 time to fit residues: 9.4105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN F 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 23644 Z= 0.229 Angle : 0.457 5.604 31958 Z= 0.244 Chirality : 0.042 0.165 3558 Planarity : 0.003 0.059 4090 Dihedral : 5.599 76.358 3240 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 3.07 % 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: 0.67 (0.15), residues: 2898 helix: 1.58 (0.16), residues: 1038 sheet: 0.02 (0.18), residues: 780 loop : -0.24 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 277 time to evaluate : 2.952 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 54 residues processed: 339 average time/residue: 1.4012 time to fit residues: 542.2352 Evaluate side-chains 311 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 257 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 52 residues processed: 4 average time/residue: 0.9758 time to fit residues: 8.5594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 242 optimal weight: 0.3980 chunk 258 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 233 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN F 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 23644 Z= 0.317 Angle : 0.498 5.682 31958 Z= 0.266 Chirality : 0.044 0.197 3558 Planarity : 0.004 0.061 4090 Dihedral : 5.696 76.846 3240 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.98 % 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: 0.55 (0.15), residues: 2898 helix: 1.46 (0.16), residues: 1038 sheet: -0.02 (0.18), residues: 780 loop : -0.30 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 264 time to evaluate : 2.991 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 46 residues processed: 323 average time/residue: 1.4977 time to fit residues: 552.0427 Evaluate side-chains 307 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 261 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 43 residues processed: 3 average time/residue: 1.2205 time to fit residues: 8.0172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.0670 chunk 273 optimal weight: 0.8980 chunk 166 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 190 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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: 0.8410 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 23644 Z= 0.129 Angle : 0.426 6.050 31958 Z= 0.228 Chirality : 0.041 0.132 3558 Planarity : 0.003 0.056 4090 Dihedral : 5.380 75.248 3240 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.04 % 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: 0.84 (0.15), residues: 2898 helix: 1.68 (0.16), residues: 1038 sheet: 0.16 (0.18), residues: 780 loop : -0.13 (0.18), residues: 1080 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 296 time to evaluate : 3.074 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 42 residues processed: 346 average time/residue: 1.3888 time to fit residues: 550.4788 Evaluate side-chains 315 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 273 time to evaluate : 2.655 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 42 residues processed: 0 time to fit residues: 3.6933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.2980 chunk 243 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.134826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110933 restraints weight = 28998.609| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.04 r_work: 0.3309 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 1.84 restraints_weight: 0.2500 r_work: 0.3282 rms_B_bonded: 1.89 restraints_weight: 0.1250 r_work: 0.3268 rms_B_bonded: 1.99 restraints_weight: 0.0625 r_work: 0.3253 rms_B_bonded: 2.13 restraints_weight: 0.0312 r_work: 0.3237 rms_B_bonded: 2.31 restraints_weight: 0.0156 r_work: 0.3220 rms_B_bonded: 2.52 restraints_weight: 0.0078 r_work: 0.3201 rms_B_bonded: 2.77 restraints_weight: 0.0039 r_work: 0.3181 rms_B_bonded: 3.06 restraints_weight: 0.0020 r_work: 0.3160 rms_B_bonded: 3.40 restraints_weight: 0.0010 r_work: 0.3137 rms_B_bonded: 3.79 restraints_weight: 0.0005 r_work: 0.3111 rms_B_bonded: 4.23 restraints_weight: 0.0002 r_work: 0.3084 rms_B_bonded: 4.73 restraints_weight: 0.0001 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23644 Z= 0.202 Angle : 0.447 5.944 31958 Z= 0.239 Chirality : 0.041 0.140 3558 Planarity : 0.003 0.056 4090 Dihedral : 5.414 74.228 3240 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.00 % 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: 0.85 (0.15), residues: 2898 helix: 1.69 (0.16), residues: 1038 sheet: 0.16 (0.18), residues: 780 loop : -0.11 (0.18), residues: 1080 =============================================================================== Job complete usr+sys time: 8631.43 seconds wall clock time: 153 minutes 50.83 seconds (9230.83 seconds total)