Starting phenix.real_space_refine on Tue Aug 6 13:14:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzh_37952/08_2024/8wzh_37952.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzh_37952/08_2024/8wzh_37952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzh_37952/08_2024/8wzh_37952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzh_37952/08_2024/8wzh_37952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzh_37952/08_2024/8wzh_37952.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wzh_37952/08_2024/8wzh_37952.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 10392 2.51 5 N 2884 2.21 5 O 3024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B ASP 498": "OD1" <-> "OD2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 249": "OD1" <-> "OD2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 290": "OE1" <-> "OE2" Residue "C PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C ASP 438": "OD1" <-> "OD2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 488": "OD1" <-> "OD2" Residue "C ASP 498": "OD1" <-> "OD2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "D PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 396": "OD1" <-> "OD2" Residue "D PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 420": "OE1" <-> "OE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D ASP 438": "OD1" <-> "OD2" Residue "D PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 488": "OD1" <-> "OD2" Residue "D ASP 498": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "A" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "C" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Chain: "D" Number of atoms: 4001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} 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: "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: "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} Time building chain proxies: 9.19, per 1000 atoms: 0.56 Number of scatterers: 16368 At special positions: 0 Unit cell: (110.21, 114.49, 86.67, 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 3024 8.00 N 2884 7.00 C 10392 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: 6.54 Conformation dependent library (CDL) restraints added in 2.9 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 40.2% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 removed outlier: 3.685A pdb=" N THR B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU B 101 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 removed outlier: 3.691A pdb=" N VAL B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 257 removed outlier: 3.605A pdb=" N GLN B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 366 removed outlier: 3.629A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU B 419 " --> pdb=" O PRO B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.855A pdb=" N LEU B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.683A pdb=" N THR A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.565A pdb=" N GLU A 101 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.692A pdb=" N VAL A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.604A pdb=" N GLN A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 348 through 366 removed outlier: 3.629A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU A 419 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.856A pdb=" N LEU A 451 " --> pdb=" O TYR A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'C' and resid 6 through 9 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 removed outlier: 3.685A pdb=" N THR C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU C 101 " --> pdb=" O LYS C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.692A pdb=" N VAL C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.605A pdb=" N GLN C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.628A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU C 419 " --> pdb=" O PRO C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.856A pdb=" N LEU C 451 " --> pdb=" O TYR C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 501 Processing helix chain 'D' and resid 6 through 9 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 54 through 65 removed outlier: 3.683A pdb=" N THR D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.564A pdb=" N GLU D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 removed outlier: 3.692A pdb=" N VAL D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 201 through 205 removed outlier: 4.020A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 257 removed outlier: 3.605A pdb=" N GLN D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 285 through 291 Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.628A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.930A pdb=" N LEU D 419 " --> pdb=" O PRO D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 removed outlier: 3.856A pdb=" N LEU D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 501 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 removed outlier: 3.738A pdb=" N ARG D 430 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.678A pdb=" N GLY B 314 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 429 through 431 removed outlier: 3.532A pdb=" N ARG B 430 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 44 removed outlier: 3.507A pdb=" N ARG C 430 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 344 removed outlier: 3.678A pdb=" N GLY A 314 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 429 through 431 removed outlier: 3.627A pdb=" N ARG A 430 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344 removed outlier: 3.678A pdb=" N GLY C 314 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE C 281 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 344 removed outlier: 3.679A pdb=" N GLY D 314 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 647 hydrogen bonds defined for protein. 1833 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: 5.27 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 6843 1.39 - 1.57: 9921 1.57 - 1.75: 20 1.75 - 1.93: 92 1.93 - 2.11: 12 Bond restraints: 16888 Sorted by residual: bond pdb=" O2B NDP D3002 " pdb=" P2B NDP D3002 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.26e+01 bond pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " ideal model delta sigma weight residual 1.833 1.616 0.217 3.80e-02 6.93e+02 3.25e+01 bond pdb=" O2B NDP A3002 " pdb=" P2B NDP A3002 " ideal model delta sigma weight residual 1.833 1.617 0.216 3.80e-02 6.93e+02 3.23e+01 bond pdb=" O2B NDP C3002 " pdb=" P2B NDP C3002 " ideal model delta sigma weight residual 1.833 1.617 0.216 3.80e-02 6.93e+02 3.23e+01 bond pdb=" O5D NDP A3002 " pdb=" PN NDP A3002 " ideal model delta sigma weight residual 1.757 1.589 0.168 3.50e-02 8.16e+02 2.30e+01 ... (remaining 16883 not shown) Histogram of bond angle deviations from ideal: 87.34 - 105.04: 626 105.04 - 122.73: 18662 122.73 - 140.43: 3744 140.43 - 158.12: 0 158.12 - 175.82: 8 Bond angle restraints: 23040 Sorted by residual: angle pdb=" O1X NDP A3002 " pdb=" P2B NDP A3002 " pdb=" O3X NDP A3002 " ideal model delta sigma weight residual 117.46 111.91 5.55 1.17e+00 7.36e-01 2.26e+01 angle pdb=" O1X NDP D3002 " pdb=" P2B NDP D3002 " pdb=" O3X NDP D3002 " ideal model delta sigma weight residual 117.46 111.96 5.50 1.17e+00 7.36e-01 2.23e+01 angle pdb=" O1X NDP B3002 " pdb=" P2B NDP B3002 " pdb=" O3X NDP B3002 " ideal model delta sigma weight residual 117.46 111.97 5.49 1.17e+00 7.36e-01 2.22e+01 angle pdb=" O1X NDP C3002 " pdb=" P2B NDP C3002 " pdb=" O3X NDP C3002 " ideal model delta sigma weight residual 117.46 112.02 5.44 1.17e+00 7.36e-01 2.18e+01 angle pdb=" O2B NDP B3002 " pdb=" P2B NDP B3002 " pdb=" O3X NDP B3002 " ideal model delta sigma weight residual 97.70 107.85 -10.15 2.45e+00 1.67e-01 1.72e+01 ... (remaining 23035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8836 17.89 - 35.78: 776 35.78 - 53.67: 148 53.67 - 71.56: 76 71.56 - 89.45: 24 Dihedral angle restraints: 9860 sinusoidal: 4080 harmonic: 5780 Sorted by residual: dihedral pdb=" CA ASN D 439 " pdb=" C ASN D 439 " pdb=" N VAL D 440 " pdb=" CA VAL D 440 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN A 439 " pdb=" C ASN A 439 " pdb=" N VAL A 440 " pdb=" CA VAL A 440 " ideal model delta harmonic sigma weight residual 180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN B 439 " pdb=" C ASN B 439 " pdb=" N VAL B 440 " pdb=" CA VAL B 440 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 960 0.040 - 0.079: 701 0.079 - 0.119: 480 0.119 - 0.159: 167 0.159 - 0.198: 20 Chirality restraints: 2328 Sorted by residual: chirality pdb=" C4D NDP D3002 " pdb=" C3D NDP D3002 " pdb=" C5D NDP D3002 " pdb=" O4D NDP D3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.20 2.00e-01 2.50e+01 9.84e-01 chirality pdb=" C4D NDP C3002 " pdb=" C3D NDP C3002 " pdb=" C5D NDP C3002 " pdb=" O4D NDP C3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" C4D NDP A3002 " pdb=" C3D NDP A3002 " pdb=" C5D NDP A3002 " pdb=" O4D NDP A3002 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 2325 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM B3001 " -0.011 2.00e-02 2.50e+03 1.34e-02 4.02e+00 pdb=" C1B HEM B3001 " 0.004 2.00e-02 2.50e+03 pdb=" C2B HEM B3001 " -0.001 2.00e-02 2.50e+03 pdb=" C3B HEM B3001 " 0.003 2.00e-02 2.50e+03 pdb=" C4B HEM B3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAB HEM B3001 " 0.020 2.00e-02 2.50e+03 pdb=" CHB HEM B3001 " 0.021 2.00e-02 2.50e+03 pdb=" CHC HEM B3001 " 0.000 2.00e-02 2.50e+03 pdb=" CMB HEM B3001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A3001 " -0.011 2.00e-02 2.50e+03 1.34e-02 4.02e+00 pdb=" C1B HEM A3001 " 0.003 2.00e-02 2.50e+03 pdb=" C2B HEM A3001 " -0.001 2.00e-02 2.50e+03 pdb=" C3B HEM A3001 " 0.003 2.00e-02 2.50e+03 pdb=" C4B HEM A3001 " -0.014 2.00e-02 2.50e+03 pdb=" CAB HEM A3001 " 0.020 2.00e-02 2.50e+03 pdb=" CHB HEM A3001 " 0.021 2.00e-02 2.50e+03 pdb=" CHC HEM A3001 " -0.000 2.00e-02 2.50e+03 pdb=" CMB HEM A3001 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM C3001 " 0.012 2.00e-02 2.50e+03 1.31e-02 3.88e+00 pdb=" C1B HEM C3001 " -0.003 2.00e-02 2.50e+03 pdb=" C2B HEM C3001 " 0.001 2.00e-02 2.50e+03 pdb=" C3B HEM C3001 " -0.003 2.00e-02 2.50e+03 pdb=" C4B HEM C3001 " 0.013 2.00e-02 2.50e+03 pdb=" CAB HEM C3001 " -0.019 2.00e-02 2.50e+03 pdb=" CHB HEM C3001 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEM C3001 " 0.000 2.00e-02 2.50e+03 pdb=" CMB HEM C3001 " 0.021 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3826 2.83 - 3.35: 16437 3.35 - 3.86: 26663 3.86 - 4.38: 32562 4.38 - 4.90: 54551 Nonbonded interactions: 134039 Sorted by model distance: nonbonded pdb=" OH TYR A 137 " pdb=" O VAL A 375 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR C 137 " pdb=" O VAL C 375 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR D 137 " pdb=" O VAL D 375 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR B 137 " pdb=" O VAL B 375 " model vdw 2.311 3.040 nonbonded pdb=" O LEU A 451 " pdb=" NH2 ARG A 456 " model vdw 2.318 3.120 ... (remaining 134034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.840 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.217 16888 Z= 0.873 Angle : 1.375 10.147 23040 Z= 0.981 Chirality : 0.070 0.198 2328 Planarity : 0.004 0.018 3052 Dihedral : 15.634 89.449 6148 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.93 % Allowed : 3.74 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.16), residues: 1980 helix: -1.14 (0.17), residues: 676 sheet: -1.12 (0.28), residues: 220 loop : -2.43 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 183 HIS 0.008 0.003 HIS C 166 PHE 0.020 0.003 PHE C 356 TYR 0.022 0.003 TYR C 489 ARG 0.005 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: B 59 ASP cc_start: 0.7180 (m-30) cc_final: 0.6839 (m-30) REVERT: B 119 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 259 ASP cc_start: 0.8290 (p0) cc_final: 0.7653 (p0) REVERT: B 260 TYR cc_start: 0.7497 (t80) cc_final: 0.7095 (t80) REVERT: B 321 ASN cc_start: 0.8352 (m-40) cc_final: 0.8136 (m-40) REVERT: B 330 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 119 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: A 259 ASP cc_start: 0.8077 (p0) cc_final: 0.7397 (p0) REVERT: A 330 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7922 (mm-30) REVERT: A 339 MET cc_start: 0.8073 (mtm) cc_final: 0.7856 (mtm) REVERT: C 59 ASP cc_start: 0.7099 (m-30) cc_final: 0.6725 (m-30) REVERT: C 119 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 259 ASP cc_start: 0.8260 (p0) cc_final: 0.7599 (p0) REVERT: C 260 TYR cc_start: 0.7509 (t80) cc_final: 0.7108 (t80) REVERT: C 321 ASN cc_start: 0.8343 (m-40) cc_final: 0.8129 (m-40) REVERT: C 330 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7927 (mm-30) REVERT: C 339 MET cc_start: 0.8066 (mtm) cc_final: 0.7860 (mtm) REVERT: D 119 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: D 259 ASP cc_start: 0.8179 (p0) cc_final: 0.7496 (p0) REVERT: D 330 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7869 (mm-30) outliers start: 16 outliers final: 4 residues processed: 217 average time/residue: 0.2975 time to fit residues: 96.2135 Evaluate side-chains 154 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS B 148 ASN B 282 GLN B 331 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 HIS A 282 GLN A 331 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 282 GLN ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS D 282 GLN D 331 GLN ** D 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16888 Z= 0.218 Angle : 0.547 4.775 23040 Z= 0.280 Chirality : 0.043 0.134 2328 Planarity : 0.004 0.039 3052 Dihedral : 8.498 93.722 2268 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.57 % Allowed : 8.00 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1980 helix: 0.73 (0.20), residues: 684 sheet: -0.13 (0.28), residues: 272 loop : -1.52 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 183 HIS 0.004 0.001 HIS C 364 PHE 0.020 0.002 PHE A 132 TYR 0.017 0.001 TYR A 489 ARG 0.003 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 2.024 Fit side-chains REVERT: B 119 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: B 236 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.8264 (p90) REVERT: B 259 ASP cc_start: 0.7766 (p0) cc_final: 0.6933 (p0) REVERT: B 260 TYR cc_start: 0.7403 (t80) cc_final: 0.7017 (t80) REVERT: B 394 MET cc_start: 0.6990 (tmm) cc_final: 0.5898 (ttt) REVERT: A 25 ASP cc_start: 0.7563 (t0) cc_final: 0.7358 (t0) REVERT: A 119 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: A 236 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (p90) REVERT: A 259 ASP cc_start: 0.7719 (p0) cc_final: 0.6927 (p0) REVERT: A 330 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7924 (mm-30) REVERT: C 25 ASP cc_start: 0.7414 (t0) cc_final: 0.7201 (t0) REVERT: C 119 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: C 236 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.8189 (p90) REVERT: C 259 ASP cc_start: 0.7756 (p0) cc_final: 0.6868 (p0) REVERT: C 260 TYR cc_start: 0.7428 (t80) cc_final: 0.7065 (t80) REVERT: D 119 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: D 236 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8093 (p90) REVERT: D 259 ASP cc_start: 0.7797 (p0) cc_final: 0.6931 (p0) REVERT: D 260 TYR cc_start: 0.7268 (t80) cc_final: 0.6881 (t80) outliers start: 44 outliers final: 25 residues processed: 189 average time/residue: 0.2474 time to fit residues: 74.2294 Evaluate side-chains 168 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 440 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 176 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 ASN A 407 ASN C 407 ASN D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 16888 Z= 0.385 Angle : 0.607 6.449 23040 Z= 0.312 Chirality : 0.046 0.151 2328 Planarity : 0.005 0.046 3052 Dihedral : 8.474 90.773 2268 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.63 % Allowed : 9.52 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.57 (0.18), residues: 1980 helix: 0.97 (0.20), residues: 684 sheet: -0.14 (0.28), residues: 272 loop : -1.42 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 183 HIS 0.005 0.001 HIS C 362 PHE 0.025 0.002 PHE C 100 TYR 0.018 0.002 TYR A 489 ARG 0.004 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.949 Fit side-chains REVERT: B 236 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8236 (p90) REVERT: B 259 ASP cc_start: 0.7837 (p0) cc_final: 0.6999 (p0) REVERT: B 394 MET cc_start: 0.6909 (tmm) cc_final: 0.6022 (tmm) REVERT: A 25 ASP cc_start: 0.7534 (t0) cc_final: 0.7332 (t0) REVERT: A 236 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8198 (p90) REVERT: A 259 ASP cc_start: 0.7795 (p0) cc_final: 0.6978 (p0) REVERT: A 260 TYR cc_start: 0.7330 (t80) cc_final: 0.6897 (t80) REVERT: A 321 ASN cc_start: 0.8426 (m-40) cc_final: 0.8216 (m-40) REVERT: A 394 MET cc_start: 0.6075 (ppp) cc_final: 0.5756 (ttp) REVERT: A 498 ASP cc_start: 0.7552 (m-30) cc_final: 0.7352 (p0) REVERT: C 236 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8196 (p90) REVERT: C 259 ASP cc_start: 0.7831 (p0) cc_final: 0.6953 (p0) REVERT: C 392 MET cc_start: 0.8526 (tpt) cc_final: 0.8003 (tpt) REVERT: C 394 MET cc_start: 0.8314 (mmt) cc_final: 0.7737 (mmt) REVERT: D 236 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8142 (p90) REVERT: D 259 ASP cc_start: 0.7953 (p0) cc_final: 0.7058 (p0) REVERT: D 392 MET cc_start: 0.8614 (tpt) cc_final: 0.8365 (tpt) REVERT: D 394 MET cc_start: 0.7196 (ttt) cc_final: 0.6571 (ttt) REVERT: D 494 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7863 (tp-100) outliers start: 45 outliers final: 36 residues processed: 164 average time/residue: 0.2504 time to fit residues: 65.4174 Evaluate side-chains 167 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 497 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16888 Z= 0.196 Angle : 0.518 4.879 23040 Z= 0.262 Chirality : 0.042 0.134 2328 Planarity : 0.004 0.045 3052 Dihedral : 7.702 89.447 2256 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.69 % Allowed : 10.81 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.18 (0.18), residues: 1980 helix: 1.30 (0.20), residues: 684 sheet: 0.21 (0.29), residues: 272 loop : -1.23 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.004 0.001 HIS A 235 PHE 0.029 0.002 PHE C 100 TYR 0.014 0.001 TYR D 489 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.926 Fit side-chains REVERT: B 236 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8329 (p90) REVERT: B 259 ASP cc_start: 0.7764 (p0) cc_final: 0.6914 (p0) REVERT: B 500 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6678 (m-80) REVERT: A 236 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8326 (p90) REVERT: A 259 ASP cc_start: 0.7732 (p0) cc_final: 0.7155 (p0) REVERT: A 394 MET cc_start: 0.5784 (ppp) cc_final: 0.5575 (ppp) REVERT: A 498 ASP cc_start: 0.7471 (m-30) cc_final: 0.7169 (p0) REVERT: C 236 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8337 (p90) REVERT: C 259 ASP cc_start: 0.7754 (p0) cc_final: 0.6891 (p0) REVERT: C 392 MET cc_start: 0.8411 (tpt) cc_final: 0.7661 (tpt) REVERT: C 394 MET cc_start: 0.8321 (mmt) cc_final: 0.7747 (mmt) REVERT: C 498 ASP cc_start: 0.7458 (m-30) cc_final: 0.7246 (p0) REVERT: D 236 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8246 (p90) REVERT: D 259 ASP cc_start: 0.7843 (p0) cc_final: 0.6968 (p0) REVERT: D 392 MET cc_start: 0.8441 (tpt) cc_final: 0.8162 (tpt) REVERT: D 394 MET cc_start: 0.7053 (ttt) cc_final: 0.6561 (ttt) REVERT: D 498 ASP cc_start: 0.7441 (m-30) cc_final: 0.7194 (p0) REVERT: D 500 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6691 (m-80) outliers start: 46 outliers final: 24 residues processed: 180 average time/residue: 0.2415 time to fit residues: 69.1979 Evaluate side-chains 167 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 0.0010 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 211 HIS A 331 GLN D 33 ASN D 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 16888 Z= 0.348 Angle : 0.596 9.233 23040 Z= 0.301 Chirality : 0.045 0.138 2328 Planarity : 0.005 0.050 3052 Dihedral : 7.869 87.262 2252 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.80 % Allowed : 10.86 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.16 (0.18), residues: 1980 helix: 1.30 (0.20), residues: 684 sheet: 0.24 (0.29), residues: 272 loop : -1.22 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 183 HIS 0.005 0.001 HIS C 362 PHE 0.029 0.002 PHE A 100 TYR 0.014 0.002 TYR C 489 ARG 0.003 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 144 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: B 236 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8386 (p90) REVERT: B 259 ASP cc_start: 0.7866 (p0) cc_final: 0.7042 (p0) REVERT: B 298 ASP cc_start: 0.7934 (t0) cc_final: 0.7509 (t0) REVERT: B 455 GLN cc_start: 0.7487 (mt0) cc_final: 0.7239 (mm-40) REVERT: B 500 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: A 236 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8360 (p90) REVERT: A 259 ASP cc_start: 0.7763 (p0) cc_final: 0.6926 (p0) REVERT: A 500 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: C 236 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8370 (p90) REVERT: C 259 ASP cc_start: 0.7880 (p0) cc_final: 0.7048 (p0) REVERT: C 298 ASP cc_start: 0.7913 (t0) cc_final: 0.7485 (t0) REVERT: C 328 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7397 (mp0) REVERT: C 392 MET cc_start: 0.8387 (tpt) cc_final: 0.7661 (tpt) REVERT: C 394 MET cc_start: 0.8374 (mmt) cc_final: 0.7822 (mmt) REVERT: C 455 GLN cc_start: 0.7401 (mt0) cc_final: 0.7173 (mm-40) REVERT: C 498 ASP cc_start: 0.7473 (m-30) cc_final: 0.7231 (p0) REVERT: C 500 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: D 236 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8291 (p90) REVERT: D 259 ASP cc_start: 0.7862 (p0) cc_final: 0.6988 (p0) REVERT: D 298 ASP cc_start: 0.7830 (t0) cc_final: 0.7412 (t0) REVERT: D 392 MET cc_start: 0.8521 (tpt) cc_final: 0.8200 (tpt) REVERT: D 394 MET cc_start: 0.7125 (ttt) cc_final: 0.6767 (ttt) REVERT: D 498 ASP cc_start: 0.7531 (m-30) cc_final: 0.7263 (p0) REVERT: D 500 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6716 (m-80) outliers start: 48 outliers final: 29 residues processed: 176 average time/residue: 0.2630 time to fit residues: 71.8186 Evaluate side-chains 176 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN C 471 GLN D 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16888 Z= 0.197 Angle : 0.528 8.136 23040 Z= 0.262 Chirality : 0.042 0.134 2328 Planarity : 0.004 0.049 3052 Dihedral : 7.559 86.017 2252 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.28 % Allowed : 12.15 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.05 (0.19), residues: 1980 helix: 1.40 (0.20), residues: 692 sheet: 0.44 (0.30), residues: 272 loop : -1.08 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.004 0.001 HIS B 235 PHE 0.029 0.002 PHE C 100 TYR 0.012 0.001 TYR C 489 ARG 0.002 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 157 time to evaluate : 1.841 Fit side-chains revert: symmetry clash REVERT: B 236 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.8325 (p90) REVERT: B 259 ASP cc_start: 0.7717 (p0) cc_final: 0.7123 (p0) REVERT: B 298 ASP cc_start: 0.7873 (t0) cc_final: 0.7439 (t0) REVERT: B 328 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7306 (mp0) REVERT: B 500 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: A 236 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8403 (p90) REVERT: A 259 ASP cc_start: 0.7717 (p0) cc_final: 0.7076 (p0) REVERT: A 498 ASP cc_start: 0.7459 (m-30) cc_final: 0.7091 (p0) REVERT: A 500 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: C 236 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8330 (p90) REVERT: C 259 ASP cc_start: 0.7736 (p0) cc_final: 0.6885 (p0) REVERT: C 298 ASP cc_start: 0.7870 (t0) cc_final: 0.7428 (t0) REVERT: C 328 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7430 (mp0) REVERT: C 392 MET cc_start: 0.8174 (tpt) cc_final: 0.7517 (tpt) REVERT: C 394 MET cc_start: 0.8417 (mmt) cc_final: 0.7853 (mmt) REVERT: C 500 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: D 236 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8325 (p90) REVERT: D 259 ASP cc_start: 0.7760 (p0) cc_final: 0.7129 (p0) REVERT: D 298 ASP cc_start: 0.7861 (t0) cc_final: 0.7414 (t0) REVERT: D 328 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7383 (mp0) REVERT: D 392 MET cc_start: 0.8500 (tpt) cc_final: 0.7892 (tpt) REVERT: D 500 TYR cc_start: 0.7058 (OUTLIER) cc_final: 0.6702 (m-80) outliers start: 39 outliers final: 27 residues processed: 177 average time/residue: 0.2657 time to fit residues: 73.1189 Evaluate side-chains 177 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 115 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16888 Z= 0.163 Angle : 0.519 7.790 23040 Z= 0.258 Chirality : 0.042 0.133 2328 Planarity : 0.004 0.049 3052 Dihedral : 7.396 83.622 2252 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.63 % Allowed : 12.44 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.21 (0.19), residues: 1980 helix: 1.55 (0.21), residues: 684 sheet: 0.61 (0.30), residues: 272 loop : -1.00 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.004 0.001 HIS D 235 PHE 0.027 0.001 PHE B 100 TYR 0.010 0.001 TYR A 489 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 160 time to evaluate : 1.826 Fit side-chains REVERT: B 236 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8363 (p90) REVERT: B 259 ASP cc_start: 0.7717 (p0) cc_final: 0.7103 (p0) REVERT: B 328 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7409 (mp0) REVERT: B 500 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: A 202 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7442 (p0) REVERT: A 236 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8365 (p90) REVERT: A 259 ASP cc_start: 0.7690 (p0) cc_final: 0.6876 (p0) REVERT: A 328 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7377 (mp0) REVERT: A 394 MET cc_start: 0.7889 (mmm) cc_final: 0.7213 (mmm) REVERT: A 500 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: C 236 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8373 (p90) REVERT: C 259 ASP cc_start: 0.7733 (p0) cc_final: 0.7108 (p0) REVERT: C 328 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7459 (mp0) REVERT: C 392 MET cc_start: 0.8078 (tpt) cc_final: 0.7420 (tpt) REVERT: C 394 MET cc_start: 0.8421 (mmt) cc_final: 0.7712 (mmt) REVERT: C 500 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: D 236 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8350 (p90) REVERT: D 259 ASP cc_start: 0.7717 (p0) cc_final: 0.7094 (p0) REVERT: D 298 ASP cc_start: 0.7867 (t0) cc_final: 0.7406 (t0) REVERT: D 328 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7454 (mp0) REVERT: D 392 MET cc_start: 0.8373 (tpt) cc_final: 0.7909 (tpp) REVERT: D 500 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6736 (m-80) outliers start: 45 outliers final: 29 residues processed: 185 average time/residue: 0.2739 time to fit residues: 76.6574 Evaluate side-chains 180 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 471 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16888 Z= 0.236 Angle : 0.543 7.298 23040 Z= 0.272 Chirality : 0.042 0.131 2328 Planarity : 0.004 0.051 3052 Dihedral : 7.487 81.959 2252 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.28 % Allowed : 13.73 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.26 (0.19), residues: 1980 helix: 1.53 (0.21), residues: 692 sheet: 0.62 (0.30), residues: 272 loop : -0.94 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 183 HIS 0.004 0.001 HIS C 364 PHE 0.021 0.002 PHE A 100 TYR 0.019 0.001 TYR A 447 ARG 0.005 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.879 Fit side-chains REVERT: B 236 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8396 (p90) REVERT: B 259 ASP cc_start: 0.7732 (p0) cc_final: 0.6889 (p0) REVERT: B 298 ASP cc_start: 0.7875 (t0) cc_final: 0.7417 (t0) REVERT: B 328 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7377 (mp0) REVERT: B 331 GLN cc_start: 0.7776 (mt0) cc_final: 0.7546 (mt0) REVERT: B 394 MET cc_start: 0.7531 (tpt) cc_final: 0.7242 (mmp) REVERT: B 500 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6752 (m-80) REVERT: A 202 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7387 (p0) REVERT: A 236 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.8395 (p90) REVERT: A 259 ASP cc_start: 0.7703 (p0) cc_final: 0.6888 (p0) REVERT: A 328 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7382 (mp0) REVERT: A 392 MET cc_start: 0.7978 (mmm) cc_final: 0.7738 (tpt) REVERT: A 500 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: C 236 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8395 (p90) REVERT: C 259 ASP cc_start: 0.7747 (p0) cc_final: 0.6915 (p0) REVERT: C 298 ASP cc_start: 0.7880 (t0) cc_final: 0.7418 (t0) REVERT: C 328 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7451 (mp0) REVERT: C 392 MET cc_start: 0.8164 (tpt) cc_final: 0.7609 (tpt) REVERT: C 394 MET cc_start: 0.8411 (mmt) cc_final: 0.7730 (mmt) REVERT: C 500 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6722 (m-80) REVERT: D 236 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8310 (p90) REVERT: D 259 ASP cc_start: 0.7719 (p0) cc_final: 0.7101 (p0) REVERT: D 298 ASP cc_start: 0.7866 (t0) cc_final: 0.7403 (t0) REVERT: D 328 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7466 (mp0) REVERT: D 392 MET cc_start: 0.8447 (tpt) cc_final: 0.7873 (tpp) REVERT: D 500 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6734 (m-80) outliers start: 39 outliers final: 29 residues processed: 173 average time/residue: 0.2603 time to fit residues: 70.0714 Evaluate side-chains 188 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16888 Z= 0.200 Angle : 0.532 7.177 23040 Z= 0.266 Chirality : 0.042 0.132 2328 Planarity : 0.004 0.050 3052 Dihedral : 7.401 80.616 2252 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.39 % Allowed : 13.73 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.30 (0.19), residues: 1980 helix: 1.53 (0.20), residues: 692 sheet: 0.62 (0.30), residues: 272 loop : -0.88 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 183 HIS 0.004 0.001 HIS D 235 PHE 0.020 0.001 PHE A 100 TYR 0.017 0.001 TYR C 447 ARG 0.004 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 1.949 Fit side-chains REVERT: B 236 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8307 (p90) REVERT: B 259 ASP cc_start: 0.7685 (p0) cc_final: 0.6843 (p0) REVERT: B 298 ASP cc_start: 0.7870 (t0) cc_final: 0.7401 (t0) REVERT: B 328 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7386 (mp0) REVERT: B 331 GLN cc_start: 0.7754 (mt0) cc_final: 0.7514 (mt0) REVERT: B 394 MET cc_start: 0.7594 (tpt) cc_final: 0.7316 (mmp) REVERT: B 500 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: A 236 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8291 (p90) REVERT: A 259 ASP cc_start: 0.7682 (p0) cc_final: 0.6868 (p0) REVERT: A 392 MET cc_start: 0.7914 (mmm) cc_final: 0.7584 (tpt) REVERT: A 500 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6863 (m-80) REVERT: C 236 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8304 (p90) REVERT: C 259 ASP cc_start: 0.7706 (p0) cc_final: 0.6864 (p0) REVERT: C 298 ASP cc_start: 0.7882 (t0) cc_final: 0.7412 (t0) REVERT: C 328 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7479 (mp0) REVERT: C 392 MET cc_start: 0.8144 (tpt) cc_final: 0.7512 (tpt) REVERT: C 394 MET cc_start: 0.8554 (mmt) cc_final: 0.7845 (mmt) REVERT: C 498 ASP cc_start: 0.7675 (m-30) cc_final: 0.7407 (p0) REVERT: C 500 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: D 236 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8307 (p90) REVERT: D 259 ASP cc_start: 0.7701 (p0) cc_final: 0.6866 (p0) REVERT: D 298 ASP cc_start: 0.7868 (t0) cc_final: 0.7399 (t0) REVERT: D 328 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7462 (mp0) REVERT: D 392 MET cc_start: 0.8392 (tpt) cc_final: 0.7833 (tpp) REVERT: D 500 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6691 (m-80) outliers start: 41 outliers final: 31 residues processed: 174 average time/residue: 0.2613 time to fit residues: 70.4414 Evaluate side-chains 188 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 0.0060 chunk 88 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 494 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16888 Z= 0.160 Angle : 0.514 6.963 23040 Z= 0.253 Chirality : 0.041 0.133 2328 Planarity : 0.004 0.049 3052 Dihedral : 7.230 77.793 2252 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.28 % Allowed : 14.14 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.19), residues: 1980 helix: 1.79 (0.20), residues: 684 sheet: 0.66 (0.30), residues: 272 loop : -0.84 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 183 HIS 0.004 0.001 HIS D 235 PHE 0.020 0.001 PHE A 100 TYR 0.016 0.001 TYR C 447 ARG 0.004 0.000 ARG B 127 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 1.835 Fit side-chains REVERT: B 236 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8282 (p90) REVERT: B 259 ASP cc_start: 0.7562 (p0) cc_final: 0.6726 (p0) REVERT: B 328 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7436 (mp0) REVERT: B 500 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: A 236 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8277 (p90) REVERT: A 259 ASP cc_start: 0.7645 (p0) cc_final: 0.6810 (p0) REVERT: A 500 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: C 236 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8282 (p90) REVERT: C 259 ASP cc_start: 0.7663 (p0) cc_final: 0.6805 (p0) REVERT: C 328 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7464 (mp0) REVERT: C 392 MET cc_start: 0.8057 (tpt) cc_final: 0.7337 (tpt) REVERT: C 394 MET cc_start: 0.8525 (mmt) cc_final: 0.7863 (mmt) REVERT: C 500 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: D 236 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.8281 (p90) REVERT: D 259 ASP cc_start: 0.7680 (p0) cc_final: 0.7068 (p0) REVERT: D 298 ASP cc_start: 0.7885 (t0) cc_final: 0.7412 (t0) REVERT: D 328 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7484 (mp0) REVERT: D 392 MET cc_start: 0.8328 (tpt) cc_final: 0.7862 (tpp) REVERT: D 500 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6787 (m-80) outliers start: 39 outliers final: 30 residues processed: 177 average time/residue: 0.2629 time to fit residues: 71.9476 Evaluate side-chains 188 residues out of total 1712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 500 TYR Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 500 TYR Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 500 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 159 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN A 331 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.089334 restraints weight = 25559.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.092052 restraints weight = 15681.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093921 restraints weight = 11583.829| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16888 Z= 0.191 Angle : 0.529 6.906 23040 Z= 0.264 Chirality : 0.042 0.132 2328 Planarity : 0.004 0.050 3052 Dihedral : 7.271 76.087 2252 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.34 % Allowed : 14.49 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.48 (0.19), residues: 1980 helix: 1.79 (0.20), residues: 684 sheet: 0.65 (0.30), residues: 272 loop : -0.81 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.004 0.001 HIS D 235 PHE 0.020 0.001 PHE A 100 TYR 0.018 0.001 TYR D 447 ARG 0.004 0.000 ARG B 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2622.68 seconds wall clock time: 48 minutes 20.35 seconds (2900.35 seconds total)