Starting phenix.real_space_refine (version: dev) on Wed Feb 22 14:53:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/02_2023/7p8w_13256_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/02_2023/7p8w_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_13256/02_2023/7p8w_13256.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/02_2023/7p8w_13256.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/02_2023/7p8w_13256_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p8w_13256/02_2023/7p8w_13256_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 18.37, per 1000 atoms: 1.04 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: 7.99 Conformation dependent library (CDL) restraints added in 4.6 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: 1.67 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: 5.14 Time building geometry restraints manager: 8.49 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 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. 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: 0.150 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: 2.350 Check model and map are aligned: 0.280 Process input model: 59.340 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 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 % 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 *********************** 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 : 2.059 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 157 average time/residue: 1.7184 time to fit residues: 296.3013 Evaluate side-chains 116 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 2.183 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.9258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 60 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 168 GLN A 449 ASN A 492 HIS B 18 GLN B 168 GLN B 449 ASN B 492 HIS C 18 GLN C 168 GLN C 449 ASN C 492 HIS D 18 GLN D 168 GLN D 449 ASN D 492 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.1548 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= 0.224 Angle : 0.633 6.412 23312 Z= 0.324 Chirality : 0.047 0.162 2352 Planarity : 0.004 0.033 3092 Dihedral : 8.771 88.855 2280 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.50 % 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: 0.37 (0.18), residues: 2012 helix: 0.66 (0.18), residues: 724 sheet: 0.78 (0.29), residues: 304 loop : -0.13 (0.19), residues: 984 *********************** 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 146 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 2.174 Fit side-chains outliers start: 26 outliers final: 8 residues processed: 140 average time/residue: 1.6690 time to fit residues: 258.0525 Evaluate side-chains 127 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.7254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 151 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 181 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.1735 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= 0.239 Angle : 0.624 5.833 23312 Z= 0.315 Chirality : 0.046 0.160 2352 Planarity : 0.005 0.035 3092 Dihedral : 8.765 89.611 2280 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 1.04 % 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: 0.62 (0.18), residues: 2012 helix: 0.87 (0.19), residues: 720 sheet: 0.97 (0.30), residues: 300 loop : 0.00 (0.20), residues: 992 *********************** 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 145 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 2.165 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 136 average time/residue: 1.7114 time to fit residues: 256.0192 Evaluate side-chains 128 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.7220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 17084 Z= 0.215 Angle : 0.586 5.683 23312 Z= 0.296 Chirality : 0.045 0.161 2352 Planarity : 0.004 0.038 3092 Dihedral : 8.542 98.296 2280 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.98 % 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: 0.67 (0.18), residues: 2012 helix: 0.88 (0.19), residues: 720 sheet: 1.08 (0.30), residues: 300 loop : 0.03 (0.20), residues: 992 *********************** 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: 17 poor density : 116 time to evaluate : 2.062 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 129 average time/residue: 1.6967 time to fit residues: 241.5654 Evaluate side-chains 123 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 2.023 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 17084 Z= 0.351 Angle : 0.684 9.426 23312 Z= 0.344 Chirality : 0.049 0.165 2352 Planarity : 0.005 0.044 3092 Dihedral : 9.596 108.712 2280 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.50 % 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: 0.45 (0.18), residues: 2012 helix: 0.68 (0.19), residues: 708 sheet: 0.94 (0.32), residues: 280 loop : -0.06 (0.19), residues: 1024 *********************** 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 141 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 2.131 Fit side-chains outliers start: 26 outliers final: 8 residues processed: 130 average time/residue: 1.7114 time to fit residues: 246.0816 Evaluate side-chains 116 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 4.0503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 211 HIS B 18 GLN B 211 HIS C 18 GLN C 211 HIS D 18 GLN D 211 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 17084 Z= 0.245 Angle : 0.601 6.209 23312 Z= 0.304 Chirality : 0.046 0.161 2352 Planarity : 0.005 0.040 3092 Dihedral : 8.892 97.855 2280 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.92 % 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: 0.55 (0.18), residues: 2012 helix: 0.79 (0.19), residues: 716 sheet: 1.09 (0.32), residues: 280 loop : -0.05 (0.19), residues: 1016 *********************** 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: 16 poor density : 112 time to evaluate : 2.086 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 128 average time/residue: 1.7022 time to fit residues: 240.7436 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 162 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 17084 Z= 0.249 Angle : 0.606 6.403 23312 Z= 0.306 Chirality : 0.046 0.161 2352 Planarity : 0.005 0.041 3092 Dihedral : 8.915 98.162 2280 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.69 % 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: 0.46 (0.18), residues: 2012 helix: 0.70 (0.19), residues: 720 sheet: 0.95 (0.32), residues: 284 loop : -0.08 (0.19), residues: 1008 *********************** 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 128 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 2.192 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 1.7212 time to fit residues: 244.4811 Evaluate side-chains 122 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.5553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 37 optimal weight: 0.0370 chunk 122 optimal weight: 8.9990 chunk 131 optimal weight: 40.0000 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 overall best weight: 6.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 17084 Z= 0.342 Angle : 0.670 8.151 23312 Z= 0.341 Chirality : 0.049 0.164 2352 Planarity : 0.005 0.046 3092 Dihedral : 9.451 103.710 2280 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.10 % 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: 0.34 (0.18), residues: 2012 helix: 0.61 (0.19), residues: 708 sheet: 0.81 (0.31), residues: 284 loop : -0.12 (0.19), residues: 1020 *********************** 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 132 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 2.016 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 128 average time/residue: 1.6481 time to fit residues: 233.9365 Evaluate side-chains 118 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.6332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 189 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17084 Z= 0.184 Angle : 0.556 5.516 23312 Z= 0.280 Chirality : 0.044 0.162 2352 Planarity : 0.004 0.037 3092 Dihedral : 8.223 91.733 2280 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.58 % 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: 0.61 (0.19), residues: 2012 helix: 0.87 (0.19), residues: 716 sheet: 0.96 (0.31), residues: 304 loop : -0.02 (0.19), residues: 992 *********************** 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 122 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 2.246 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 122 average time/residue: 1.6261 time to fit residues: 220.2141 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.6919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.1955 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= 0.231 Angle : 0.595 5.630 23312 Z= 0.299 Chirality : 0.045 0.161 2352 Planarity : 0.005 0.041 3092 Dihedral : 8.590 94.692 2280 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.52 % 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: 0.79 (0.19), residues: 716 sheet: 1.01 (0.32), residues: 284 loop : -0.06 (0.19), residues: 1012 ********************** 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 121 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 2.176 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 120 average time/residue: 1.6986 time to fit residues: 226.1461 Evaluate side-chains 120 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 2.9044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN B 18 GLN C 18 GLN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.077269 restraints weight = 35104.366| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.53 r_work: 0.2694 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 17084 Z= 0.225 Angle : 0.589 5.790 23312 Z= 0.295 Chirality : 0.045 0.160 2352 Planarity : 0.004 0.040 3092 Dihedral : 8.508 93.971 2280 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.58 % 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: 0.77 (0.19), residues: 716 sheet: 1.02 (0.32), residues: 284 loop : -0.05 (0.19), residues: 1012 =============================================================================== Job complete usr+sys time: 5125.18 seconds wall clock time: 92 minutes 44.25 seconds (5564.25 seconds total)