Starting phenix.real_space_refine on Sun Mar 17 12:05:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/03_2024/7p8w_13256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/03_2024/7p8w_13256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/03_2024/7p8w_13256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/03_2024/7p8w_13256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/03_2024/7p8w_13256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/03_2024/7p8w_13256_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.031 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 Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10504 2.51 5 N 2920 2.21 5 O 4176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D ASP 128": "OD1" <-> "OD2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17668 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "B" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "C" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "D" Number of atoms: 4047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} Conformer: "B" Number of residues, atoms: 502, 4037 Classifications: {'peptide': 502} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 464} bond proxies already assigned to first conformer: 4145 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 281 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 279 Classifications: {'water': 279} Link IDs: {None: 278} Conformer: "B" Number of residues, atoms: 279, 279 Classifications: {'water': 279} Link IDs: {None: 278} Chain: "B" Number of atoms: 280 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Conformer: "B" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Chain: "C" Number of atoms: 277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Conformer: "B" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Chain: "D" Number of atoms: 278 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Conformer: "B" Number of residues, atoms: 277, 277 Classifications: {'water': 277} Link IDs: {None: 276} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AHIS A 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 372 " occ=0.50 residue: pdb=" N AHIS B 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 372 " occ=0.50 residue: pdb=" N AHIS C 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS C 372 " occ=0.50 residue: pdb=" N AHIS D 372 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 372 " occ=0.50 residue: pdb=" O AHOH A 858 " occ=0.50 pdb=" O BHOH A 858 " occ=0.50 residue: pdb=" O AHOH A 965 " occ=0.50 pdb=" O BHOH A 965 " occ=0.50 residue: pdb=" O AHOH B 857 " occ=0.50 pdb=" O BHOH B 857 " occ=0.50 residue: pdb=" O AHOH B 964 " occ=0.50 pdb=" O BHOH B 964 " occ=0.50 residue: pdb=" O AHOH C 853 " occ=0.50 pdb=" O BHOH C 853 " occ=0.50 residue: pdb=" O AHOH D 847 " occ=0.50 pdb=" O BHOH D 847 " occ=0.50 Time building chain proxies: 17.72, per 1000 atoms: 1.00 Number of scatterers: 17668 At special positions: 0 Unit cell: (108.102, 110.242, 84.5547, 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) Fe 4 26.01 S 52 16.00 P 12 15.00 O 4176 8.00 N 2920 7.00 C 10504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.61 Conformation dependent library (CDL) restraints added in 5.7 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 4 sheets defined 35.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.539A pdb=" N ARG A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 158 through 168 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 179 through 188 Processing helix chain 'A' and resid 190 through 200 removed outlier: 4.170A pdb=" N HIS A 194 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.503A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.736A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix removed outlier: 3.558A pdb=" N HIS A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 453 through 469 removed outlier: 5.196A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.507A pdb=" N VAL A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 503 Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.539A pdb=" N ARG B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 158 through 168 Proline residue: B 162 - end of helix Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 190 through 200 removed outlier: 4.170A pdb=" N HIS B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.504A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 325 through 328 No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 349 through 365 removed outlier: 3.736A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix removed outlier: 3.558A pdb=" N HIS B 364 " --> pdb=" O ASP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'B' and resid 453 through 469 removed outlier: 5.196A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.507A pdb=" N VAL B 485 " --> pdb=" O ASN B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 503 Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 55 through 66 removed outlier: 3.540A pdb=" N ARG C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 158 through 168 Proline residue: C 162 - end of helix Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 190 through 200 removed outlier: 4.170A pdb=" N HIS C 194 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 209 through 211 No H-bonds generated for 'chain 'C' and resid 209 through 211' Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.504A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 325 through 328 No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 349 through 365 removed outlier: 3.736A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Proline residue: C 359 - end of helix removed outlier: 3.558A pdb=" N HIS C 364 " --> pdb=" O ASP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 441 through 449 Processing helix chain 'C' and resid 453 through 469 removed outlier: 5.196A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.507A pdb=" N VAL C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 503 Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.539A pdb=" N ARG D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 158 through 168 Proline residue: D 162 - end of helix Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 190 through 200 removed outlier: 4.170A pdb=" N HIS D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.504A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 325 through 328 No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 349 through 365 removed outlier: 3.736A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR D 358 " --> pdb=" O ARG D 354 " (cutoff:3.500A) Proline residue: D 359 - end of helix removed outlier: 3.557A pdb=" N HIS D 364 " --> pdb=" O ASP D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 441 through 449 Processing helix chain 'D' and resid 453 through 469 removed outlier: 5.196A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.508A pdb=" N VAL D 485 " --> pdb=" O ASN D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 503 Processing sheet with id= A, first strand: chain 'A' and resid 141 through 148 removed outlier: 7.066A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 279 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 315 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP A 277 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 141 through 148 removed outlier: 7.066A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 279 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS B 315 " --> pdb=" O TRP B 277 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP B 277 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 141 through 148 removed outlier: 7.065A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 141 through 148 removed outlier: 7.066A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE D 279 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS D 315 " --> pdb=" O TRP D 277 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP D 277 " --> pdb=" O LYS D 315 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1392 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: 4.84 Time building geometry restraints manager: 9.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 5922 1.37 - 1.55: 11038 1.55 - 1.73: 20 1.73 - 1.91: 92 1.91 - 2.09: 12 Bond restraints: 17084 Sorted by residual: bond pdb=" O2B NDP B 601 " pdb=" P2B NDP B 601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.29e+01 bond pdb=" O2B NDP D 601 " pdb=" P2B NDP D 601 " ideal model delta sigma weight residual 1.833 1.615 0.218 3.80e-02 6.93e+02 3.28e+01 bond pdb=" O2B NDP A 601 " pdb=" P2B NDP A 601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.28e+01 bond pdb=" O2B NDP C 601 " pdb=" P2B NDP C 601 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.27e+01 bond pdb=" O5D NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 1.757 1.589 0.168 3.50e-02 8.16e+02 2.29e+01 ... (remaining 17079 not shown) Histogram of bond angle deviations from ideal: 87.68 - 105.79: 686 105.79 - 123.89: 20111 123.89 - 142.00: 2507 142.00 - 160.11: 0 160.11 - 178.22: 8 Bond angle restraints: 23312 Sorted by residual: angle pdb=" PA NDP A 601 " pdb=" O3 NDP A 601 " pdb=" PN NDP A 601 " ideal model delta sigma weight residual 107.74 134.07 -26.33 1.95e+00 2.62e-01 1.82e+02 angle pdb=" PA NDP D 601 " pdb=" O3 NDP D 601 " pdb=" PN NDP D 601 " ideal model delta sigma weight residual 107.74 134.07 -26.33 1.95e+00 2.62e-01 1.82e+02 angle pdb=" PA NDP B 601 " pdb=" O3 NDP B 601 " pdb=" PN NDP B 601 " ideal model delta sigma weight residual 107.74 134.06 -26.32 1.95e+00 2.62e-01 1.81e+02 angle pdb=" PA NDP C 601 " pdb=" O3 NDP C 601 " pdb=" PN NDP C 601 " ideal model delta sigma weight residual 107.74 134.06 -26.32 1.95e+00 2.62e-01 1.81e+02 angle pdb=" C5B NDP C 601 " pdb=" O5B NDP C 601 " pdb=" PA NDP C 601 " ideal model delta sigma weight residual 103.84 119.78 -15.94 1.91e+00 2.73e-01 6.93e+01 ... (remaining 23307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 9341 21.02 - 42.04: 491 42.04 - 63.06: 100 63.06 - 84.09: 44 84.09 - 105.11: 12 Dihedral angle restraints: 9988 sinusoidal: 4132 harmonic: 5856 Sorted by residual: dihedral pdb=" CA ILE B 281 " pdb=" C ILE B 281 " pdb=" N GLN B 282 " pdb=" CA GLN B 282 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ILE A 281 " pdb=" C ILE A 281 " pdb=" N GLN A 282 " pdb=" CA GLN A 282 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ILE C 281 " pdb=" C ILE C 281 " pdb=" N GLN C 282 " pdb=" CA GLN C 282 " ideal model delta harmonic sigma weight residual 180.00 155.72 24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 9985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1162 0.064 - 0.128: 819 0.128 - 0.192: 326 0.192 - 0.256: 37 0.256 - 0.320: 8 Chirality restraints: 2352 Sorted by residual: chirality pdb=" CA TYR B 236 " pdb=" N TYR B 236 " pdb=" C TYR B 236 " pdb=" CB TYR B 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR C 236 " pdb=" N TYR C 236 " pdb=" C TYR C 236 " pdb=" CB TYR C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA TYR D 236 " pdb=" N TYR D 236 " pdb=" C TYR D 236 " pdb=" CB TYR D 236 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 2349 not shown) Planarity restraints: 3092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP C 601 " -0.075 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" C3N NDP C 601 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NDP C 601 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP C 601 " 0.050 2.00e-02 2.50e+03 pdb=" N1N NDP C 601 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP B 601 " 0.074 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" C3N NDP B 601 " 0.031 2.00e-02 2.50e+03 pdb=" C4N NDP B 601 " 0.007 2.00e-02 2.50e+03 pdb=" C7N NDP B 601 " -0.049 2.00e-02 2.50e+03 pdb=" N1N NDP B 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP D 601 " -0.075 2.00e-02 2.50e+03 5.10e-02 3.26e+01 pdb=" C3N NDP D 601 " -0.031 2.00e-02 2.50e+03 pdb=" C4N NDP D 601 " -0.007 2.00e-02 2.50e+03 pdb=" C7N NDP D 601 " 0.049 2.00e-02 2.50e+03 pdb=" N1N NDP D 601 " 0.063 2.00e-02 2.50e+03 ... (remaining 3089 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5796 2.85 - 3.36: 18635 3.36 - 3.88: 38064 3.88 - 4.39: 44680 4.39 - 4.90: 67359 Nonbonded interactions: 174534 Sorted by model distance: nonbonded pdb=" ND1 HIS C 364 " pdb=" O HOH C 701 " model vdw 2.340 2.520 nonbonded pdb=" ND1 HIS B 364 " pdb=" O HOH B 701 " model vdw 2.341 2.520 nonbonded pdb=" ND1 HIS D 364 " pdb=" O HOH D 701 " model vdw 2.342 2.520 nonbonded pdb=" ND1 HIS A 364 " pdb=" O HOH A 701 " model vdw 2.342 2.520 nonbonded pdb=" OE1 GLU A 191 " pdb=" O HOH A 702 " model vdw 2.413 2.440 ... (remaining 174529 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' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) selection = (chain 'C' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 4 through 371 or resid 373 through 505 or resid 601 throug \ h 602)) } 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=0.50 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.660 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 62.460 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 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 : 0.014 0.218 17084 Z= 0.944 Angle : 1.791 26.335 23312 Z= 1.239 Chirality : 0.089 0.320 2352 Planarity : 0.008 0.051 3092 Dihedral : 14.824 105.107 6228 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.80 % Favored : 96.00 % Rotamer: Outliers : 0.75 % Allowed : 3.87 % Favored : 95.38 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 2.70 % 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: -1.36 (0.16), residues: 2012 helix: -1.24 (0.15), residues: 692 sheet: 0.15 (0.28), residues: 284 loop : -0.86 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.009 TRP D 15 HIS 0.014 0.005 HIS D 75 PHE 0.051 0.008 PHE D 82 TYR 0.042 0.008 TYR B 236 ARG 0.018 0.003 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 2.014 Fit side-chains REVERT: A 18 GLN cc_start: 0.8170 (mt0) cc_final: 0.7910 (mp10) REVERT: A 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7793 (ptmm) REVERT: A 248 GLU cc_start: 0.8528 (tt0) cc_final: 0.8162 (mp0) REVERT: A 273 LYS cc_start: 0.8810 (mttp) cc_final: 0.8463 (mtpt) REVERT: A 306 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8454 (mppt) REVERT: A 339 MET cc_start: 0.9072 (mtm) cc_final: 0.8517 (mtm) REVERT: A 382 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8444 (ttm-80) REVERT: B 18 GLN cc_start: 0.8168 (mt0) cc_final: 0.7909 (mp10) REVERT: B 23 LYS cc_start: 0.8088 (tttt) cc_final: 0.7793 (ptmm) REVERT: B 248 GLU cc_start: 0.8525 (tt0) cc_final: 0.8162 (mp0) REVERT: B 273 LYS cc_start: 0.8811 (mttp) cc_final: 0.8465 (mtpt) REVERT: B 306 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8453 (mppt) REVERT: B 339 MET cc_start: 0.9078 (mtm) cc_final: 0.8531 (mtm) REVERT: B 382 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8431 (ttm-80) REVERT: C 18 GLN cc_start: 0.8169 (mt0) cc_final: 0.7910 (mp10) REVERT: C 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7790 (ptmm) REVERT: C 248 GLU cc_start: 0.8527 (tt0) cc_final: 0.8163 (mp0) REVERT: C 273 LYS cc_start: 0.8813 (mttp) cc_final: 0.8467 (mtpt) REVERT: C 306 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8456 (mppt) REVERT: C 339 MET cc_start: 0.9072 (mtm) cc_final: 0.8517 (mtm) REVERT: C 382 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8430 (ttm-80) REVERT: D 18 GLN cc_start: 0.8169 (mt0) cc_final: 0.7910 (mp10) REVERT: D 23 LYS cc_start: 0.8087 (tttt) cc_final: 0.7791 (ptmm) REVERT: D 248 GLU cc_start: 0.8524 (tt0) cc_final: 0.8160 (mp0) REVERT: D 273 LYS cc_start: 0.8809 (mttp) cc_final: 0.8463 (mtpt) REVERT: D 306 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8454 (mppt) REVERT: D 339 MET cc_start: 0.9078 (mtm) cc_final: 0.8533 (mtm) REVERT: D 382 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8431 (ttm-80) outliers start: 13 outliers final: 4 residues processed: 157 average time/residue: 1.6944 time to fit residues: 291.8876 Evaluate side-chains 116 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain D residue 138 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 449 ASN A 492 HIS B 168 GLN B 449 ASN B 492 HIS C 168 GLN C 449 ASN C 492 HIS D 168 GLN D 449 ASN D 492 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17084 Z= 0.273 Angle : 0.668 7.883 23312 Z= 0.342 Chirality : 0.049 0.163 2352 Planarity : 0.005 0.034 3092 Dihedral : 9.293 98.835 2284 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.44 % Allowed : 5.14 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.32 (0.18), residues: 2012 helix: 0.59 (0.18), residues: 708 sheet: 0.78 (0.29), residues: 300 loop : -0.13 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 183 HIS 0.006 0.002 HIS A 209 PHE 0.023 0.003 PHE C 164 TYR 0.031 0.002 TYR C 236 ARG 0.004 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 2.026 Fit side-chains REVERT: A 18 GLN cc_start: 0.8014 (mt0) cc_final: 0.7774 (mp10) REVERT: A 248 GLU cc_start: 0.8409 (tt0) cc_final: 0.7981 (mp0) REVERT: A 273 LYS cc_start: 0.8786 (mttp) cc_final: 0.8437 (mtmt) REVERT: A 306 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8447 (mppt) REVERT: B 18 GLN cc_start: 0.8010 (mt0) cc_final: 0.7772 (mp10) REVERT: B 248 GLU cc_start: 0.8410 (tt0) cc_final: 0.7983 (mp0) REVERT: B 273 LYS cc_start: 0.8786 (mttp) cc_final: 0.8437 (mtmt) REVERT: B 306 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8443 (mppt) REVERT: C 18 GLN cc_start: 0.8011 (mt0) cc_final: 0.7773 (mp10) REVERT: C 248 GLU cc_start: 0.8410 (tt0) cc_final: 0.7983 (mp0) REVERT: C 273 LYS cc_start: 0.8789 (mttp) cc_final: 0.8440 (mtmt) REVERT: C 306 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8450 (mppt) REVERT: D 18 GLN cc_start: 0.8014 (mt0) cc_final: 0.7774 (mp10) REVERT: D 248 GLU cc_start: 0.8406 (tt0) cc_final: 0.7980 (mp0) REVERT: D 273 LYS cc_start: 0.8784 (mttp) cc_final: 0.8436 (mtmt) REVERT: D 306 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8450 (mppt) REVERT: D 394 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7493 (mpt) outliers start: 25 outliers final: 8 residues processed: 132 average time/residue: 1.5427 time to fit residues: 225.8278 Evaluate side-chains 126 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 394 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 20.0000 chunk 56 optimal weight: 0.1980 chunk 151 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 0.4980 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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: 0.8938 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17084 Z= 0.176 Angle : 0.564 5.746 23312 Z= 0.284 Chirality : 0.044 0.159 2352 Planarity : 0.004 0.032 3092 Dihedral : 8.120 89.494 2284 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.52 % Allowed : 6.52 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2012 helix: 1.04 (0.19), residues: 720 sheet: 1.03 (0.30), residues: 300 loop : 0.06 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 183 HIS 0.004 0.001 HIS A 218 PHE 0.015 0.002 PHE C 164 TYR 0.024 0.002 TYR D 236 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 2.127 Fit side-chains REVERT: A 18 GLN cc_start: 0.8006 (mt0) cc_final: 0.7760 (mp10) REVERT: A 23 LYS cc_start: 0.8211 (ttpp) cc_final: 0.7914 (tttp) REVERT: A 248 GLU cc_start: 0.8188 (tt0) cc_final: 0.7894 (mp0) REVERT: A 273 LYS cc_start: 0.8672 (mttp) cc_final: 0.8367 (mtpt) REVERT: A 306 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8569 (tttm) REVERT: A 499 LYS cc_start: 0.8241 (mtpp) cc_final: 0.8025 (tttm) REVERT: A 503 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6510 (tm-30) REVERT: B 18 GLN cc_start: 0.8003 (mt0) cc_final: 0.7760 (mp10) REVERT: B 23 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7915 (tttp) REVERT: B 248 GLU cc_start: 0.8187 (tt0) cc_final: 0.7894 (mp0) REVERT: B 273 LYS cc_start: 0.8673 (mttp) cc_final: 0.8369 (mtpt) REVERT: B 306 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8569 (tttm) REVERT: B 499 LYS cc_start: 0.8245 (mtpp) cc_final: 0.8028 (tttm) REVERT: B 503 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6510 (tm-30) REVERT: C 18 GLN cc_start: 0.8006 (mt0) cc_final: 0.7761 (mp10) REVERT: C 23 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7915 (tttp) REVERT: C 248 GLU cc_start: 0.8192 (tt0) cc_final: 0.7899 (mp0) REVERT: C 273 LYS cc_start: 0.8673 (mttp) cc_final: 0.8369 (mtpt) REVERT: C 306 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8569 (tttm) REVERT: C 394 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7127 (mpt) REVERT: C 499 LYS cc_start: 0.8240 (mtpp) cc_final: 0.8024 (tttm) REVERT: C 503 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6510 (tm-30) REVERT: D 18 GLN cc_start: 0.8005 (mt0) cc_final: 0.7760 (mp10) REVERT: D 23 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7917 (tttp) REVERT: D 128 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8904 (m-30) REVERT: D 248 GLU cc_start: 0.8187 (tt0) cc_final: 0.7895 (mp0) REVERT: D 273 LYS cc_start: 0.8671 (mttp) cc_final: 0.8368 (mtpt) REVERT: D 306 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8570 (tttm) REVERT: D 499 LYS cc_start: 0.8240 (mtpp) cc_final: 0.8024 (tttm) REVERT: D 503 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6510 (tm-30) outliers start: 9 outliers final: 4 residues processed: 132 average time/residue: 1.7534 time to fit residues: 254.4232 Evaluate side-chains 123 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 394 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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: 0.8969 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17084 Z= 0.303 Angle : 0.654 8.705 23312 Z= 0.329 Chirality : 0.048 0.163 2352 Planarity : 0.005 0.039 3092 Dihedral : 9.278 101.426 2280 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.92 % Allowed : 6.81 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.18), residues: 2012 helix: 0.78 (0.19), residues: 708 sheet: 0.93 (0.31), residues: 284 loop : -0.04 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 183 HIS 0.008 0.002 HIS D 218 PHE 0.020 0.003 PHE A 136 TYR 0.029 0.002 TYR C 236 ARG 0.004 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 2.111 Fit side-chains REVERT: A 18 GLN cc_start: 0.8010 (mt0) cc_final: 0.7747 (mp10) REVERT: A 23 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7941 (tttp) REVERT: A 248 GLU cc_start: 0.8286 (tt0) cc_final: 0.7858 (mp0) REVERT: A 273 LYS cc_start: 0.8820 (mttp) cc_final: 0.8438 (mtpt) REVERT: A 306 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8579 (tttm) REVERT: A 499 LYS cc_start: 0.8323 (mtpp) cc_final: 0.8066 (tttm) REVERT: B 18 GLN cc_start: 0.8008 (mt0) cc_final: 0.7746 (mp10) REVERT: B 23 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7942 (tttp) REVERT: B 248 GLU cc_start: 0.8284 (tt0) cc_final: 0.7857 (mp0) REVERT: B 273 LYS cc_start: 0.8820 (mttp) cc_final: 0.8440 (mtpt) REVERT: B 306 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8580 (tttm) REVERT: B 499 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8067 (tttm) REVERT: C 18 GLN cc_start: 0.8009 (mt0) cc_final: 0.7747 (mp10) REVERT: C 23 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7941 (tttp) REVERT: C 248 GLU cc_start: 0.8286 (tt0) cc_final: 0.7859 (mp0) REVERT: C 273 LYS cc_start: 0.8822 (mttp) cc_final: 0.8441 (mtpt) REVERT: C 306 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8580 (tttm) REVERT: C 499 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8067 (tttm) REVERT: D 18 GLN cc_start: 0.8013 (mt0) cc_final: 0.7748 (mp10) REVERT: D 23 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7939 (tttp) REVERT: D 248 GLU cc_start: 0.8284 (tt0) cc_final: 0.7859 (mp0) REVERT: D 273 LYS cc_start: 0.8818 (mttp) cc_final: 0.8437 (mtpt) REVERT: D 306 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8581 (tttm) REVERT: D 499 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8084 (tttm) outliers start: 16 outliers final: 4 residues processed: 125 average time/residue: 1.7214 time to fit residues: 236.7107 Evaluate side-chains 116 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.0970 chunk 109 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 overall best weight: 4.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 HIS C 211 HIS D 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17084 Z= 0.244 Angle : 0.603 6.780 23312 Z= 0.304 Chirality : 0.046 0.160 2352 Planarity : 0.005 0.039 3092 Dihedral : 8.899 97.884 2280 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.98 % Allowed : 7.22 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.53 (0.18), residues: 2012 helix: 0.74 (0.19), residues: 720 sheet: 1.03 (0.32), residues: 280 loop : -0.02 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 183 HIS 0.008 0.001 HIS A 218 PHE 0.017 0.002 PHE A 136 TYR 0.027 0.002 TYR C 236 ARG 0.003 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 2.049 Fit side-chains REVERT: A 18 GLN cc_start: 0.8004 (mt0) cc_final: 0.7741 (mp10) REVERT: A 23 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7943 (tttp) REVERT: A 248 GLU cc_start: 0.8273 (tt0) cc_final: 0.7881 (mp0) REVERT: A 273 LYS cc_start: 0.8748 (mttp) cc_final: 0.8376 (mtpt) REVERT: A 306 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8587 (tttm) REVERT: A 454 GLU cc_start: 0.8287 (mp0) cc_final: 0.8023 (mp0) REVERT: A 503 GLU cc_start: 0.6627 (mt-10) cc_final: 0.6335 (tm-30) REVERT: B 18 GLN cc_start: 0.8004 (mt0) cc_final: 0.7742 (mp10) REVERT: B 23 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7943 (tttp) REVERT: B 248 GLU cc_start: 0.8275 (tt0) cc_final: 0.7881 (mp0) REVERT: B 273 LYS cc_start: 0.8748 (mttp) cc_final: 0.8378 (mtpt) REVERT: B 306 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8588 (tttm) REVERT: B 454 GLU cc_start: 0.8284 (mp0) cc_final: 0.8044 (mp0) REVERT: B 503 GLU cc_start: 0.6612 (mt-10) cc_final: 0.6325 (tm-30) REVERT: C 18 GLN cc_start: 0.8004 (mt0) cc_final: 0.7741 (mp10) REVERT: C 23 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7929 (tttp) REVERT: C 248 GLU cc_start: 0.8274 (tt0) cc_final: 0.7883 (mp0) REVERT: C 273 LYS cc_start: 0.8750 (mttp) cc_final: 0.8378 (mtpt) REVERT: C 306 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8588 (tttm) REVERT: C 454 GLU cc_start: 0.8286 (mp0) cc_final: 0.8045 (mp0) REVERT: C 503 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6336 (tm-30) REVERT: D 18 GLN cc_start: 0.8005 (mt0) cc_final: 0.7741 (mp10) REVERT: D 23 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7942 (tttp) REVERT: D 248 GLU cc_start: 0.8273 (tt0) cc_final: 0.7881 (mp0) REVERT: D 273 LYS cc_start: 0.8746 (mttp) cc_final: 0.8375 (mtpt) REVERT: D 306 LYS cc_start: 0.8859 (mtpt) cc_final: 0.8589 (tttm) REVERT: D 454 GLU cc_start: 0.8282 (mp0) cc_final: 0.8021 (mp0) REVERT: D 503 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6337 (tm-30) outliers start: 17 outliers final: 4 residues processed: 129 average time/residue: 1.7525 time to fit residues: 249.4459 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 193 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.8960 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17084 Z= 0.265 Angle : 0.619 6.883 23312 Z= 0.313 Chirality : 0.047 0.162 2352 Planarity : 0.005 0.041 3092 Dihedral : 9.039 99.953 2280 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.69 % Allowed : 7.51 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.47 (0.18), residues: 2012 helix: 0.69 (0.19), residues: 720 sheet: 0.99 (0.32), residues: 280 loop : -0.05 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 183 HIS 0.008 0.002 HIS B 218 PHE 0.018 0.002 PHE A 136 TYR 0.028 0.002 TYR D 236 ARG 0.003 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.724 Fit side-chains REVERT: A 18 GLN cc_start: 0.8005 (mt0) cc_final: 0.7741 (mp10) REVERT: A 23 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7962 (tttp) REVERT: A 248 GLU cc_start: 0.8264 (tt0) cc_final: 0.7872 (mp0) REVERT: A 273 LYS cc_start: 0.8750 (mttp) cc_final: 0.8380 (mtpt) REVERT: A 306 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8586 (tttm) REVERT: A 454 GLU cc_start: 0.8310 (mp0) cc_final: 0.8071 (mp0) REVERT: A 503 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6300 (tm-30) REVERT: B 18 GLN cc_start: 0.8005 (mt0) cc_final: 0.7742 (mp10) REVERT: B 23 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7960 (tttp) REVERT: B 248 GLU cc_start: 0.8272 (tt0) cc_final: 0.7872 (mp0) REVERT: B 273 LYS cc_start: 0.8749 (mttp) cc_final: 0.8381 (mtpt) REVERT: B 306 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8587 (tttm) REVERT: B 454 GLU cc_start: 0.8310 (mp0) cc_final: 0.8073 (mp0) REVERT: B 503 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6302 (tm-30) REVERT: C 18 GLN cc_start: 0.8006 (mt0) cc_final: 0.7743 (mp10) REVERT: C 23 LYS cc_start: 0.8205 (ttpp) cc_final: 0.7960 (tttp) REVERT: C 248 GLU cc_start: 0.8268 (tt0) cc_final: 0.7875 (mp0) REVERT: C 273 LYS cc_start: 0.8750 (mttp) cc_final: 0.8381 (mtpt) REVERT: C 306 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8579 (tttm) REVERT: C 454 GLU cc_start: 0.8312 (mp0) cc_final: 0.8074 (mp0) REVERT: C 503 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6299 (tm-30) REVERT: D 18 GLN cc_start: 0.8007 (mt0) cc_final: 0.7742 (mp10) REVERT: D 23 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7958 (tttp) REVERT: D 248 GLU cc_start: 0.8271 (tt0) cc_final: 0.7871 (mp0) REVERT: D 273 LYS cc_start: 0.8747 (mttp) cc_final: 0.8379 (mtpt) REVERT: D 306 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8588 (tttm) REVERT: D 454 GLU cc_start: 0.8304 (mp0) cc_final: 0.8067 (mp0) REVERT: D 503 GLU cc_start: 0.6546 (mt-10) cc_final: 0.6300 (tm-30) outliers start: 12 outliers final: 4 residues processed: 124 average time/residue: 1.6435 time to fit residues: 225.2796 Evaluate side-chains 123 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17084 Z= 0.271 Angle : 0.617 7.138 23312 Z= 0.311 Chirality : 0.047 0.162 2352 Planarity : 0.005 0.041 3092 Dihedral : 9.034 99.514 2280 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.64 % Allowed : 7.33 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.47 (0.18), residues: 2012 helix: 0.68 (0.19), residues: 720 sheet: 0.99 (0.32), residues: 280 loop : -0.05 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 183 HIS 0.007 0.001 HIS C 218 PHE 0.018 0.002 PHE B 136 TYR 0.028 0.002 TYR C 236 ARG 0.004 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 2.222 Fit side-chains REVERT: A 18 GLN cc_start: 0.8027 (mt0) cc_final: 0.7758 (mp10) REVERT: A 23 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7973 (tttm) REVERT: A 248 GLU cc_start: 0.8269 (tt0) cc_final: 0.7874 (mp0) REVERT: A 273 LYS cc_start: 0.8745 (mttp) cc_final: 0.8373 (mtpt) REVERT: A 306 LYS cc_start: 0.8854 (mtpt) cc_final: 0.8586 (tttm) REVERT: A 454 GLU cc_start: 0.8315 (mp0) cc_final: 0.8076 (mp0) REVERT: A 503 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6317 (tm-30) REVERT: B 18 GLN cc_start: 0.8006 (mt0) cc_final: 0.7742 (mp10) REVERT: B 23 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7973 (tttm) REVERT: B 248 GLU cc_start: 0.8272 (tt0) cc_final: 0.7876 (mp0) REVERT: B 273 LYS cc_start: 0.8744 (mttp) cc_final: 0.8374 (mtpt) REVERT: B 306 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8586 (tttm) REVERT: B 454 GLU cc_start: 0.8312 (mp0) cc_final: 0.8075 (mp0) REVERT: B 503 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6315 (tm-30) REVERT: C 18 GLN cc_start: 0.8007 (mt0) cc_final: 0.7742 (mp10) REVERT: C 23 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7973 (tttm) REVERT: C 248 GLU cc_start: 0.8272 (tt0) cc_final: 0.7877 (mp0) REVERT: C 273 LYS cc_start: 0.8746 (mttp) cc_final: 0.8375 (mtpt) REVERT: C 306 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8580 (tttm) REVERT: C 454 GLU cc_start: 0.8314 (mp0) cc_final: 0.8077 (mp0) REVERT: C 503 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6317 (tm-30) REVERT: D 18 GLN cc_start: 0.8029 (mt0) cc_final: 0.7759 (mp10) REVERT: D 23 LYS cc_start: 0.8187 (ttpp) cc_final: 0.7972 (tttm) REVERT: D 248 GLU cc_start: 0.8271 (tt0) cc_final: 0.7874 (mp0) REVERT: D 273 LYS cc_start: 0.8743 (mttp) cc_final: 0.8372 (mtpt) REVERT: D 306 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8581 (tttm) REVERT: D 454 GLU cc_start: 0.8306 (mp0) cc_final: 0.8069 (mp0) REVERT: D 503 GLU cc_start: 0.6603 (mt-10) cc_final: 0.6318 (tm-30) outliers start: 11 outliers final: 4 residues processed: 127 average time/residue: 1.7069 time to fit residues: 238.8563 Evaluate side-chains 124 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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: 0.8938 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17084 Z= 0.199 Angle : 0.560 5.569 23312 Z= 0.282 Chirality : 0.044 0.161 2352 Planarity : 0.004 0.038 3092 Dihedral : 8.265 93.526 2280 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.29 % Allowed : 7.56 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.65 (0.18), residues: 2012 helix: 0.89 (0.19), residues: 716 sheet: 1.13 (0.32), residues: 280 loop : 0.00 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 183 HIS 0.006 0.001 HIS D 218 PHE 0.014 0.002 PHE A 136 TYR 0.025 0.002 TYR A 236 ARG 0.002 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 2.167 Fit side-chains REVERT: A 18 GLN cc_start: 0.8006 (mt0) cc_final: 0.7738 (mp10) REVERT: A 23 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7974 (tttm) REVERT: A 248 GLU cc_start: 0.8237 (tt0) cc_final: 0.7874 (mp0) REVERT: A 273 LYS cc_start: 0.8693 (mttp) cc_final: 0.8328 (mtpt) REVERT: A 306 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8567 (tttm) REVERT: A 454 GLU cc_start: 0.8343 (mp0) cc_final: 0.8096 (mp0) REVERT: A 503 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6303 (tm-30) REVERT: B 18 GLN cc_start: 0.8004 (mt0) cc_final: 0.7738 (mp10) REVERT: B 23 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7973 (tttm) REVERT: B 248 GLU cc_start: 0.8213 (tt0) cc_final: 0.7873 (mp0) REVERT: B 273 LYS cc_start: 0.8692 (mttp) cc_final: 0.8329 (mtpt) REVERT: B 306 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8568 (tttm) REVERT: B 454 GLU cc_start: 0.8344 (mp0) cc_final: 0.8099 (mp0) REVERT: B 503 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6303 (tm-30) REVERT: C 18 GLN cc_start: 0.8005 (mt0) cc_final: 0.7738 (mp10) REVERT: C 23 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7983 (tttm) REVERT: C 248 GLU cc_start: 0.8242 (tt0) cc_final: 0.7880 (mp0) REVERT: C 273 LYS cc_start: 0.8694 (mttp) cc_final: 0.8329 (mtpt) REVERT: C 306 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8568 (tttm) REVERT: C 454 GLU cc_start: 0.8345 (mp0) cc_final: 0.8099 (mp0) REVERT: C 503 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6305 (tm-30) REVERT: D 18 GLN cc_start: 0.8006 (mt0) cc_final: 0.7737 (mp10) REVERT: D 23 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7971 (tttm) REVERT: D 248 GLU cc_start: 0.8237 (tt0) cc_final: 0.7875 (mp0) REVERT: D 273 LYS cc_start: 0.8690 (mttp) cc_final: 0.8327 (mtpt) REVERT: D 306 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8569 (tttm) REVERT: D 454 GLU cc_start: 0.8343 (mp0) cc_final: 0.8097 (mp0) REVERT: D 503 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6304 (tm-30) outliers start: 5 outliers final: 4 residues processed: 124 average time/residue: 1.7440 time to fit residues: 238.3616 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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: 0.8948 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17084 Z= 0.229 Angle : 0.588 5.634 23312 Z= 0.296 Chirality : 0.045 0.161 2352 Planarity : 0.004 0.040 3092 Dihedral : 8.571 95.326 2280 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.23 % Allowed : 7.97 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2012 helix: 0.80 (0.19), residues: 716 sheet: 1.01 (0.32), residues: 280 loop : -0.01 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 183 HIS 0.007 0.001 HIS B 218 PHE 0.016 0.002 PHE B 136 TYR 0.026 0.002 TYR D 236 ARG 0.003 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.230 Fit side-chains REVERT: A 18 GLN cc_start: 0.8032 (mt0) cc_final: 0.7759 (mp10) REVERT: A 23 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7981 (tttm) REVERT: A 248 GLU cc_start: 0.8242 (tt0) cc_final: 0.7877 (mp0) REVERT: A 273 LYS cc_start: 0.8720 (mttp) cc_final: 0.8356 (mtpt) REVERT: A 306 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8571 (tttm) REVERT: A 454 GLU cc_start: 0.8292 (mp0) cc_final: 0.8045 (mp0) REVERT: A 503 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6281 (tm-30) REVERT: B 18 GLN cc_start: 0.8010 (mt0) cc_final: 0.7741 (mp10) REVERT: B 23 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7980 (tttm) REVERT: B 248 GLU cc_start: 0.8219 (tt0) cc_final: 0.7874 (mp0) REVERT: B 273 LYS cc_start: 0.8719 (mttp) cc_final: 0.8357 (mtpt) REVERT: B 306 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8571 (tttm) REVERT: B 454 GLU cc_start: 0.8289 (mp0) cc_final: 0.8044 (mp0) REVERT: B 503 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6280 (tm-30) REVERT: C 18 GLN cc_start: 0.8012 (mt0) cc_final: 0.7742 (mp10) REVERT: C 23 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7981 (tttm) REVERT: C 248 GLU cc_start: 0.8247 (tt0) cc_final: 0.7880 (mp0) REVERT: C 273 LYS cc_start: 0.8720 (mttp) cc_final: 0.8357 (mtpt) REVERT: C 306 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8570 (tttm) REVERT: C 454 GLU cc_start: 0.8291 (mp0) cc_final: 0.8045 (mp0) REVERT: C 503 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6281 (tm-30) REVERT: D 18 GLN cc_start: 0.8012 (mt0) cc_final: 0.7741 (mp10) REVERT: D 23 LYS cc_start: 0.8190 (ttpp) cc_final: 0.7978 (tttm) REVERT: D 248 GLU cc_start: 0.8244 (tt0) cc_final: 0.7878 (mp0) REVERT: D 273 LYS cc_start: 0.8718 (mttp) cc_final: 0.8356 (mtpt) REVERT: D 306 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8571 (tttm) REVERT: D 454 GLU cc_start: 0.8288 (mp0) cc_final: 0.8042 (mp0) REVERT: D 503 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6282 (tm-30) outliers start: 4 outliers final: 4 residues processed: 120 average time/residue: 1.6785 time to fit residues: 222.3611 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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: 0.8942 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17084 Z= 0.216 Angle : 0.576 5.574 23312 Z= 0.288 Chirality : 0.045 0.160 2352 Planarity : 0.004 0.039 3092 Dihedral : 8.435 94.445 2280 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.23 % Allowed : 7.97 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.59 (0.18), residues: 2012 helix: 0.82 (0.19), residues: 716 sheet: 1.05 (0.32), residues: 280 loop : -0.00 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 183 HIS 0.006 0.001 HIS D 218 PHE 0.015 0.002 PHE A 136 TYR 0.025 0.002 TYR A 236 ARG 0.002 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.231 Fit side-chains REVERT: A 18 GLN cc_start: 0.8031 (mt0) cc_final: 0.7758 (mp10) REVERT: A 23 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7983 (tttm) REVERT: A 248 GLU cc_start: 0.8212 (tt0) cc_final: 0.7874 (mp0) REVERT: A 273 LYS cc_start: 0.8710 (mttp) cc_final: 0.8348 (mtpt) REVERT: A 306 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8572 (tttm) REVERT: A 454 GLU cc_start: 0.8292 (mp0) cc_final: 0.8046 (mp0) REVERT: A 503 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6273 (tm-30) REVERT: B 18 GLN cc_start: 0.8007 (mt0) cc_final: 0.7739 (mp10) REVERT: B 23 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7982 (tttm) REVERT: B 248 GLU cc_start: 0.8216 (tt0) cc_final: 0.7874 (mp0) REVERT: B 273 LYS cc_start: 0.8708 (mttp) cc_final: 0.8347 (mtpt) REVERT: B 306 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8580 (tttm) REVERT: B 454 GLU cc_start: 0.8290 (mp0) cc_final: 0.8045 (mp0) REVERT: B 503 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6271 (tm-30) REVERT: C 18 GLN cc_start: 0.8031 (mt0) cc_final: 0.7758 (mp10) REVERT: C 23 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7983 (tttm) REVERT: C 248 GLU cc_start: 0.8215 (tt0) cc_final: 0.7878 (mp0) REVERT: C 273 LYS cc_start: 0.8710 (mttp) cc_final: 0.8348 (mtpt) REVERT: C 306 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8568 (tttm) REVERT: C 454 GLU cc_start: 0.8291 (mp0) cc_final: 0.8046 (mp0) REVERT: C 503 GLU cc_start: 0.6577 (mt-10) cc_final: 0.6274 (tm-30) REVERT: D 18 GLN cc_start: 0.8010 (mt0) cc_final: 0.7739 (mp10) REVERT: D 23 LYS cc_start: 0.8192 (ttpp) cc_final: 0.7980 (tttm) REVERT: D 248 GLU cc_start: 0.8211 (tt0) cc_final: 0.7875 (mp0) REVERT: D 273 LYS cc_start: 0.8707 (mttp) cc_final: 0.8346 (mtpt) REVERT: D 306 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8569 (tttm) REVERT: D 454 GLU cc_start: 0.8289 (mp0) cc_final: 0.8043 (mp0) REVERT: D 503 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6274 (tm-30) outliers start: 4 outliers final: 4 residues processed: 120 average time/residue: 1.7339 time to fit residues: 229.1707 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.078814 restraints weight = 35355.817| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.55 r_work: 0.2719 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17084 Z= 0.181 Angle : 0.546 5.495 23312 Z= 0.272 Chirality : 0.044 0.161 2352 Planarity : 0.004 0.038 3092 Dihedral : 7.804 90.554 2280 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.23 % Allowed : 7.97 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.71 (0.19), residues: 2012 helix: 0.92 (0.19), residues: 716 sheet: 1.02 (0.31), residues: 300 loop : 0.08 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 183 HIS 0.005 0.001 HIS B 218 PHE 0.013 0.002 PHE A 136 TYR 0.023 0.002 TYR C 500 ARG 0.002 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5210.12 seconds wall clock time: 93 minutes 50.29 seconds (5630.29 seconds total)