Starting phenix.real_space_refine on Mon Feb 19 00:41:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/02_2024/7s66_24851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/02_2024/7s66_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_24851/02_2024/7s66_24851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/02_2024/7s66_24851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/02_2024/7s66_24851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s66_24851/02_2024/7s66_24851_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 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. 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-5238/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: 11.14, per 1000 atoms: 0.48 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: 8.04 Conformation dependent library (CDL) restraints added in 4.0 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: 5.21 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: 8.14 Time building geometry restraints manager: 8.71 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 - 17.95: 13664 17.95 - 35.90: 514 35.90 - 53.85: 150 53.85 - 71.80: 54 71.80 - 89.74: 24 Dihedral angle restraints: 14406 sinusoidal: 6090 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 14403 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 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: 0.290 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: 0.020 Extract box with map and model: 2.890 Check model and map are aligned: 0.310 Set scattering table: 0.210 Process input model: 58.880 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 12.056 89.744 9066 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.016 TRP B 92 HIS 0.007 0.002 HIS D 423 PHE 0.050 0.009 PHE F 237 TYR 0.064 0.013 TYR E 235 ARG 0.010 0.001 ARG C 161 *********************** 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 : 2.815 Fit side-chains REVERT: A 235 TYR cc_start: 0.8980 (m-80) cc_final: 0.8648 (m-80) REVERT: A 404 LYS cc_start: 0.8205 (mttt) cc_final: 0.7994 (mttm) REVERT: B 487 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7185 (mt-10) REVERT: C 487 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7090 (mm-30) REVERT: D 235 TYR cc_start: 0.8987 (m-80) cc_final: 0.8649 (m-80) REVERT: D 273 MET cc_start: 0.8715 (mtp) cc_final: 0.8481 (mtm) REVERT: E 281 ASP cc_start: 0.7122 (m-30) cc_final: 0.6610 (m-30) REVERT: E 362 ILE cc_start: 0.8826 (mt) cc_final: 0.8580 (mp) REVERT: E 487 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7192 (mt-10) REVERT: F 487 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7121 (mm-30) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 1.7662 time to fit residues: 1202.4174 Evaluate side-chains 319 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.775 ------------------------------------------------------------------------------- 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: 3.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 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: 0.7981 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23644 Z= 0.160 Angle : 0.483 5.958 31958 Z= 0.270 Chirality : 0.042 0.134 3558 Planarity : 0.003 0.032 4090 Dihedral : 10.776 73.419 3612 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.94 % Allowed : 10.51 % Favored : 86.55 % 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: 0.99 (0.15), residues: 2898 helix: 1.22 (0.16), residues: 1044 sheet: 0.53 (0.19), residues: 774 loop : 0.38 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 92 HIS 0.006 0.001 HIS E 463 PHE 0.020 0.001 PHE D 301 TYR 0.014 0.002 TYR D 132 ARG 0.009 0.001 ARG F 340 *********************** 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 431 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 359 time to evaluate : 2.619 Fit side-chains REVERT: A 357 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: A 404 LYS cc_start: 0.8389 (mttt) cc_final: 0.8149 (mttm) REVERT: A 426 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7620 (t) REVERT: B 487 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7105 (mt-10) REVERT: C 228 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8302 (p) REVERT: C 393 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7189 (mtm110) REVERT: C 426 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7653 (t) REVERT: C 487 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7024 (mm-30) REVERT: D 357 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: D 426 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7590 (t) REVERT: E 362 ILE cc_start: 0.8865 (mt) cc_final: 0.8616 (mp) REVERT: E 487 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7082 (mt-10) REVERT: F 228 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (p) REVERT: F 393 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7054 (mtm110) REVERT: F 487 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7175 (mt-10) outliers start: 72 outliers final: 18 residues processed: 415 average time/residue: 1.4577 time to fit residues: 685.9211 Evaluate side-chains 311 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 284 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.0770 chunk 81 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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: 0.8078 moved from start: 0.2925 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= 0.269 Angle : 0.490 5.931 31958 Z= 0.269 Chirality : 0.043 0.154 3558 Planarity : 0.003 0.025 4090 Dihedral : 11.055 89.043 3612 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.07 % Allowed : 11.24 % Favored : 85.69 % 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: 1.06 (0.16), residues: 2898 helix: 1.70 (0.16), residues: 1008 sheet: 0.27 (0.18), residues: 780 loop : 0.26 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 92 HIS 0.011 0.001 HIS E 463 PHE 0.027 0.002 PHE D 301 TYR 0.014 0.002 TYR D 235 ARG 0.009 0.001 ARG C 340 *********************** 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 388 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 313 time to evaluate : 3.124 Fit side-chains REVERT: A 269 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7186 (tmt170) REVERT: A 404 LYS cc_start: 0.8395 (mttt) cc_final: 0.8105 (mttm) REVERT: B 106 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8660 (tt) REVERT: B 357 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: B 480 LYS cc_start: 0.7849 (mttm) cc_final: 0.7565 (mttm) REVERT: B 487 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7266 (mt-10) REVERT: C 202 ASP cc_start: 0.7652 (m-30) cc_final: 0.7448 (m-30) REVERT: C 217 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7924 (ttt90) REVERT: C 357 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: C 393 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7187 (mtm110) REVERT: C 426 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7974 (t) REVERT: C 487 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 269 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7169 (tmt170) REVERT: E 106 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8617 (tt) REVERT: E 362 ILE cc_start: 0.8917 (mt) cc_final: 0.8697 (mp) REVERT: E 471 MET cc_start: 0.7345 (mpp) cc_final: 0.7026 (mpt) REVERT: E 487 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7245 (mt-10) REVERT: F 217 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7917 (ttt90) REVERT: F 357 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: F 393 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7179 (mtm110) REVERT: F 487 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7260 (mt-10) outliers start: 75 outliers final: 36 residues processed: 383 average time/residue: 1.5910 time to fit residues: 685.8283 Evaluate side-chains 311 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 263 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 249 optimal weight: 0.0060 chunk 75 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23644 Z= 0.129 Angle : 0.417 5.552 31958 Z= 0.230 Chirality : 0.041 0.134 3558 Planarity : 0.003 0.036 4090 Dihedral : 10.219 89.605 3612 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.86 % Allowed : 12.51 % Favored : 84.63 % 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: 1.06 (0.16), residues: 2898 helix: 1.59 (0.16), residues: 1044 sheet: 0.34 (0.19), residues: 786 loop : 0.26 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 92 HIS 0.003 0.000 HIS E 463 PHE 0.020 0.001 PHE C 301 TYR 0.010 0.001 TYR A 154 ARG 0.008 0.000 ARG A 340 *********************** 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 378 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 308 time to evaluate : 2.494 Fit side-chains REVERT: A 269 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7129 (tmt170) REVERT: A 404 LYS cc_start: 0.8322 (mttt) cc_final: 0.8079 (mttm) REVERT: B 487 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7228 (mt-10) REVERT: C 217 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7998 (ttt90) REVERT: C 357 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: C 393 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7448 (mtm110) REVERT: C 487 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7193 (mt-10) REVERT: D 269 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7188 (tmt170) REVERT: D 310 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: E 362 ILE cc_start: 0.8930 (mt) cc_final: 0.8699 (mp) REVERT: E 487 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7173 (mt-10) REVERT: F 202 ASP cc_start: 0.7703 (m-30) cc_final: 0.7486 (m-30) REVERT: F 217 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7990 (ttt90) REVERT: F 357 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: F 393 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7454 (mtm110) REVERT: F 487 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7208 (mt-10) outliers start: 70 outliers final: 35 residues processed: 368 average time/residue: 1.5938 time to fit residues: 658.2117 Evaluate side-chains 306 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 262 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 249 optimal weight: 0.0000 chunk 70 optimal weight: 8.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- 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 C 361 GLN D 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 23644 Z= 0.464 Angle : 0.592 6.572 31958 Z= 0.316 Chirality : 0.047 0.229 3558 Planarity : 0.004 0.040 4090 Dihedral : 11.226 85.361 3612 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.84 % Allowed : 13.21 % Favored : 82.95 % 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: 0.52 (0.15), residues: 2898 helix: 1.33 (0.16), residues: 1038 sheet: -0.05 (0.18), residues: 780 loop : -0.18 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 92 HIS 0.007 0.001 HIS D 463 PHE 0.033 0.003 PHE F 301 TYR 0.017 0.002 TYR B 235 ARG 0.008 0.001 ARG F 340 *********************** 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 386 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 292 time to evaluate : 2.682 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8094 (t80) cc_final: 0.7858 (t80) REVERT: A 404 LYS cc_start: 0.8238 (mttt) cc_final: 0.7953 (mttm) REVERT: A 475 LYS cc_start: 0.8364 (mmmt) cc_final: 0.8156 (mmtt) REVERT: A 480 LYS cc_start: 0.8055 (mttm) cc_final: 0.7825 (mttm) REVERT: B 487 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 488 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7658 (mtm-85) REVERT: C 54 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8594 (tt) REVERT: C 124 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7555 (t) REVERT: C 217 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8052 (ttt90) REVERT: C 393 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7252 (mtm110) REVERT: C 487 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7349 (mt-10) REVERT: D 88 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7937 (tpt-90) REVERT: D 132 TYR cc_start: 0.8117 (t80) cc_final: 0.7887 (t80) REVERT: E 362 ILE cc_start: 0.8993 (mt) cc_final: 0.8739 (mp) REVERT: E 471 MET cc_start: 0.7434 (mpp) cc_final: 0.7197 (mpt) REVERT: E 487 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7469 (mt-10) REVERT: E 488 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7643 (mtm-85) REVERT: F 54 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8596 (tt) REVERT: F 124 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7451 (t) REVERT: F 217 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8057 (ttt90) REVERT: F 393 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7247 (mtm110) REVERT: F 487 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7329 (mt-10) outliers start: 94 outliers final: 49 residues processed: 369 average time/residue: 1.6609 time to fit residues: 685.4009 Evaluate side-chains 319 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 261 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 124 SER Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 231 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23644 Z= 0.208 Angle : 0.446 5.593 31958 Z= 0.244 Chirality : 0.042 0.141 3558 Planarity : 0.003 0.028 4090 Dihedral : 10.499 86.389 3612 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.31 % Allowed : 14.10 % Favored : 82.58 % 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: 1.54 (0.16), residues: 1038 sheet: 0.00 (0.18), residues: 780 loop : -0.16 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 92 HIS 0.002 0.000 HIS A 463 PHE 0.021 0.002 PHE C 301 TYR 0.012 0.001 TYR C 235 ARG 0.007 0.000 ARG E 311 *********************** 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 372 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 291 time to evaluate : 2.490 Fit side-chains revert: symmetry clash REVERT: A 132 TYR cc_start: 0.8122 (t80) cc_final: 0.7856 (t80) REVERT: A 269 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7177 (tmt170) REVERT: A 362 ILE cc_start: 0.9030 (mt) cc_final: 0.8711 (mm) REVERT: A 404 LYS cc_start: 0.8239 (mttt) cc_final: 0.7961 (mttm) REVERT: A 431 GLU cc_start: 0.7837 (pt0) cc_final: 0.7624 (mt-10) REVERT: B 487 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7335 (mt-10) REVERT: B 488 ARG cc_start: 0.7888 (mtm110) cc_final: 0.7607 (mtp85) REVERT: C 54 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8526 (tt) REVERT: C 217 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8048 (ttt90) REVERT: C 357 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: C 393 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7177 (mtm110) REVERT: C 487 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7336 (mt-10) REVERT: D 132 TYR cc_start: 0.8072 (t80) cc_final: 0.7826 (t80) REVERT: D 269 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7188 (tmt170) REVERT: D 362 ILE cc_start: 0.9023 (mt) cc_final: 0.8704 (mm) REVERT: E 471 MET cc_start: 0.7410 (mpp) cc_final: 0.7184 (mpt) REVERT: E 487 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7429 (mt-10) REVERT: E 488 ARG cc_start: 0.7874 (mtm110) cc_final: 0.7596 (mtp85) REVERT: F 54 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8522 (tt) REVERT: F 106 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8349 (tt) REVERT: F 217 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8051 (ttt90) REVERT: F 357 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: F 393 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7175 (mtm110) REVERT: F 487 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7334 (mt-10) outliers start: 81 outliers final: 48 residues processed: 359 average time/residue: 1.6196 time to fit residues: 652.4766 Evaluate side-chains 323 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 264 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23644 Z= 0.293 Angle : 0.491 8.114 31958 Z= 0.265 Chirality : 0.043 0.153 3558 Planarity : 0.003 0.032 4090 Dihedral : 10.374 86.219 3612 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.31 % Allowed : 14.64 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 2898 helix: 1.51 (0.16), residues: 1038 sheet: 0.00 (0.18), residues: 780 loop : -0.19 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 92 HIS 0.003 0.001 HIS D 463 PHE 0.025 0.002 PHE C 301 TYR 0.013 0.002 TYR B 235 ARG 0.006 0.001 ARG A 162 *********************** 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 357 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 276 time to evaluate : 2.628 Fit side-chains revert: symmetry clash REVERT: A 269 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7186 (tmt170) REVERT: A 362 ILE cc_start: 0.9047 (mt) cc_final: 0.8706 (mm) REVERT: A 404 LYS cc_start: 0.8347 (mttt) cc_final: 0.8068 (mttm) REVERT: B 487 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7362 (mt-10) REVERT: B 488 ARG cc_start: 0.7901 (mtm110) cc_final: 0.7626 (mtp85) REVERT: C 54 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8545 (tt) REVERT: C 106 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8366 (tt) REVERT: C 217 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8039 (ttt90) REVERT: C 357 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7468 (pt0) REVERT: C 393 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7211 (mtm110) REVERT: C 431 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: C 487 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7371 (mt-10) REVERT: D 132 TYR cc_start: 0.8115 (t80) cc_final: 0.7843 (t80) REVERT: D 269 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7247 (tmt170) REVERT: D 362 ILE cc_start: 0.9042 (mt) cc_final: 0.8719 (mm) REVERT: E 487 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7365 (mt-10) REVERT: E 488 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7619 (mtp85) REVERT: F 54 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8543 (tt) REVERT: F 106 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8349 (tt) REVERT: F 217 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8044 (ttt90) REVERT: F 357 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7470 (pt0) REVERT: F 393 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7211 (mtm110) REVERT: F 487 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7372 (mt-10) outliers start: 81 outliers final: 48 residues processed: 343 average time/residue: 1.6181 time to fit residues: 622.9448 Evaluate side-chains 316 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 255 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 493 SER 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: 2.9990 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8101 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23644 Z= 0.158 Angle : 0.426 5.448 31958 Z= 0.232 Chirality : 0.041 0.137 3558 Planarity : 0.003 0.049 4090 Dihedral : 9.721 88.514 3612 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.03 % Allowed : 15.04 % Favored : 81.93 % 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: 0.83 (0.16), residues: 2898 helix: 1.70 (0.16), residues: 1038 sheet: 0.11 (0.18), residues: 780 loop : -0.14 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 92 HIS 0.002 0.000 HIS E 463 PHE 0.017 0.001 PHE C 301 TYR 0.010 0.001 TYR C 235 ARG 0.013 0.000 ARG F 340 *********************** 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 367 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 293 time to evaluate : 3.007 Fit side-chains revert: symmetry clash REVERT: A 269 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7273 (tmt170) REVERT: A 357 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: A 362 ILE cc_start: 0.9033 (mt) cc_final: 0.8718 (mm) REVERT: A 404 LYS cc_start: 0.8339 (mttt) cc_final: 0.8068 (mttm) REVERT: B 487 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7317 (mt-10) REVERT: B 488 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7568 (mtp85) REVERT: C 54 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8458 (tt) REVERT: C 106 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8388 (tt) REVERT: C 217 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8069 (ttt90) REVERT: C 357 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: C 374 ARG cc_start: 0.8273 (mtt180) cc_final: 0.8024 (mtt180) REVERT: C 393 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7156 (mtm110) REVERT: C 487 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7323 (mt-10) REVERT: D 132 TYR cc_start: 0.8120 (t80) cc_final: 0.7835 (t80) REVERT: D 269 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7248 (tmt170) REVERT: D 357 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: D 362 ILE cc_start: 0.9017 (mt) cc_final: 0.8742 (mm) REVERT: E 362 ILE cc_start: 0.8998 (mt) cc_final: 0.8653 (mp) REVERT: E 487 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7309 (mt-10) REVERT: E 488 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7565 (mtp85) REVERT: F 54 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8493 (tt) REVERT: F 106 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8380 (tt) REVERT: F 217 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8064 (ttt90) REVERT: F 357 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: F 374 ARG cc_start: 0.8275 (mtt180) cc_final: 0.8023 (mtt180) REVERT: F 393 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7168 (mtm110) REVERT: F 487 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7319 (mt-10) outliers start: 74 outliers final: 39 residues processed: 354 average time/residue: 1.5764 time to fit residues: 628.8594 Evaluate side-chains 329 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 495 THR Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 426 THR Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 471 MET Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 242 optimal weight: 0.0770 chunk 258 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 233 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 F 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23644 Z= 0.262 Angle : 0.469 6.399 31958 Z= 0.253 Chirality : 0.042 0.145 3558 Planarity : 0.003 0.052 4090 Dihedral : 9.851 89.537 3612 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.82 % Allowed : 15.13 % Favored : 82.05 % 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: 0.76 (0.15), residues: 2898 helix: 1.65 (0.16), residues: 1038 sheet: 0.10 (0.18), residues: 780 loop : -0.18 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 92 HIS 0.002 0.001 HIS D 463 PHE 0.024 0.002 PHE C 301 TYR 0.011 0.001 TYR B 235 ARG 0.015 0.001 ARG E 340 *********************** 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 343 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 274 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.7404 (ptm) cc_final: 0.7181 (ptm) REVERT: A 269 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7313 (tmt170) REVERT: A 357 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: A 362 ILE cc_start: 0.9031 (mt) cc_final: 0.8771 (mm) REVERT: A 404 LYS cc_start: 0.8353 (mttt) cc_final: 0.8071 (mttm) REVERT: B 362 ILE cc_start: 0.9140 (mt) cc_final: 0.8888 (mp) REVERT: B 487 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7357 (mt-10) REVERT: B 488 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7603 (mtp85) REVERT: C 54 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8532 (tt) REVERT: C 106 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 217 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7986 (ttt90) REVERT: C 357 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: C 393 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7169 (mtm110) REVERT: C 487 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7363 (mt-10) REVERT: D 21 MET cc_start: 0.7398 (ptm) cc_final: 0.7181 (ptm) REVERT: D 132 TYR cc_start: 0.8162 (t80) cc_final: 0.7859 (t80) REVERT: D 269 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7307 (tmt170) REVERT: D 357 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7381 (pt0) REVERT: D 362 ILE cc_start: 0.9037 (mt) cc_final: 0.8700 (mm) REVERT: E 487 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7347 (mt-10) REVERT: E 488 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7602 (mtp85) REVERT: F 54 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8523 (tt) REVERT: F 106 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8384 (tt) REVERT: F 217 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7994 (ttt90) REVERT: F 357 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: F 393 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7173 (mtm110) REVERT: F 487 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7365 (mt-10) outliers start: 69 outliers final: 40 residues processed: 330 average time/residue: 1.6282 time to fit residues: 601.9987 Evaluate side-chains 317 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 263 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 426 THR Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 426 THR Chi-restraints excluded: chain F residue 471 MET Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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: 0.8101 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23644 Z= 0.150 Angle : 0.426 6.446 31958 Z= 0.231 Chirality : 0.041 0.135 3558 Planarity : 0.003 0.047 4090 Dihedral : 9.262 87.124 3612 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.21 % Allowed : 15.90 % Favored : 81.89 % 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: 0.90 (0.16), residues: 2898 helix: 1.76 (0.16), residues: 1038 sheet: 0.18 (0.18), residues: 780 loop : -0.11 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 92 HIS 0.002 0.000 HIS B 463 PHE 0.018 0.001 PHE C 301 TYR 0.009 0.001 TYR F 235 ARG 0.011 0.000 ARG F 340 ********************** 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 329 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 275 time to evaluate : 2.894 Fit side-chains revert: symmetry clash REVERT: A 269 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7277 (tmt170) REVERT: A 357 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: A 362 ILE cc_start: 0.9009 (mt) cc_final: 0.8751 (mm) REVERT: A 404 LYS cc_start: 0.8333 (mttt) cc_final: 0.8047 (mttm) REVERT: B 162 ARG cc_start: 0.7664 (ttp80) cc_final: 0.7163 (ttp80) REVERT: B 362 ILE cc_start: 0.9122 (mt) cc_final: 0.8859 (mp) REVERT: B 487 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7361 (mt-10) REVERT: C 54 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8497 (tt) REVERT: C 106 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 217 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8035 (ttt90) REVERT: C 281 ASP cc_start: 0.6999 (m-30) cc_final: 0.6796 (m-30) REVERT: C 357 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: C 374 ARG cc_start: 0.8255 (mtt180) cc_final: 0.8011 (mtt180) REVERT: C 393 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7457 (mtm110) REVERT: C 487 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 132 TYR cc_start: 0.8158 (t80) cc_final: 0.7866 (t80) REVERT: D 269 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7361 (tmt170) REVERT: D 357 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: D 362 ILE cc_start: 0.9010 (mt) cc_final: 0.8744 (mm) REVERT: E 362 ILE cc_start: 0.8949 (mt) cc_final: 0.8698 (mp) REVERT: E 487 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7315 (mt-10) REVERT: E 488 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7580 (mtp85) REVERT: F 54 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8484 (tt) REVERT: F 106 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8385 (tt) REVERT: F 217 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8040 (ttt90) REVERT: F 357 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: F 374 ARG cc_start: 0.8253 (mtt180) cc_final: 0.8007 (mtt180) REVERT: F 393 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7456 (mtm110) REVERT: F 487 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7317 (mt-10) outliers start: 54 outliers final: 35 residues processed: 323 average time/residue: 1.6987 time to fit residues: 615.2955 Evaluate side-chains 318 residues out of total 2472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 217 ARG Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 393 ARG Chi-restraints excluded: chain C residue 426 THR Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 269 ARG Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 379 SER Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 217 ARG Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain F residue 471 MET Chi-restraints excluded: chain F residue 493 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 210 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 361 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110366 restraints weight = 29026.841| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.03 r_work: 0.3183 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23644 Z= 0.274 Angle : 0.473 6.579 31958 Z= 0.255 Chirality : 0.042 0.146 3558 Planarity : 0.003 0.048 4090 Dihedral : 9.578 89.151 3612 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.41 % Allowed : 15.82 % Favored : 81.77 % 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: 0.78 (0.15), residues: 2898 helix: 1.66 (0.16), residues: 1038 sheet: 0.11 (0.18), residues: 780 loop : -0.18 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 92 HIS 0.003 0.001 HIS D 463 PHE 0.024 0.002 PHE C 301 TYR 0.011 0.002 TYR B 235 ARG 0.011 0.001 ARG F 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9880.90 seconds wall clock time: 175 minutes 32.24 seconds (10532.24 seconds total)