Starting phenix.real_space_refine on Fri Feb 16 00:02:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/02_2024/7k24_22642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/02_2024/7k24_22642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/02_2024/7k24_22642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/02_2024/7k24_22642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/02_2024/7k24_22642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k24_22642/02_2024/7k24_22642.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 1.000 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8695 2.51 5 N 2300 2.21 5 O 2675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F1 GLU 35": "OE1" <-> "OE2" Residue "F1 ASP 44": "OD1" <-> "OD2" Residue "F1 GLU 50": "OE1" <-> "OE2" Residue "F1 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 68": "OE1" <-> "OE2" Residue "F1 GLU 87": "OE1" <-> "OE2" Residue "F1 ASP 111": "OD1" <-> "OD2" Residue "F1 GLU 170": "OE1" <-> "OE2" Residue "F1 ASP 173": "OD1" <-> "OD2" Residue "F1 ASP 180": "OD1" <-> "OD2" Residue "F1 GLU 187": "OE1" <-> "OE2" Residue "F1 GLU 188": "OE1" <-> "OE2" Residue "F1 ASP 219": "OD1" <-> "OD2" Residue "F1 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 GLU 342": "OE1" <-> "OE2" Residue "F1 GLU 344": "OE1" <-> "OE2" Residue "F1 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F1 ASP 355": "OD1" <-> "OD2" Residue "F1 GLU 358": "OE1" <-> "OE2" Residue "F1 ASP 365": "OD1" <-> "OD2" Residue "F1 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 35": "OE1" <-> "OE2" Residue "F2 ASP 44": "OD1" <-> "OD2" Residue "F2 GLU 50": "OE1" <-> "OE2" Residue "F2 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 68": "OE1" <-> "OE2" Residue "F2 GLU 87": "OE1" <-> "OE2" Residue "F2 ASP 111": "OD1" <-> "OD2" Residue "F2 GLU 170": "OE1" <-> "OE2" Residue "F2 ASP 173": "OD1" <-> "OD2" Residue "F2 ASP 180": "OD1" <-> "OD2" Residue "F2 GLU 187": "OE1" <-> "OE2" Residue "F2 GLU 188": "OE1" <-> "OE2" Residue "F2 ASP 219": "OD1" <-> "OD2" Residue "F2 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 342": "OE1" <-> "OE2" Residue "F2 GLU 344": "OE1" <-> "OE2" Residue "F2 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 ASP 355": "OD1" <-> "OD2" Residue "F2 GLU 358": "OE1" <-> "OE2" Residue "F2 ASP 365": "OD1" <-> "OD2" Residue "F2 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 35": "OE1" <-> "OE2" Residue "F3 ASP 44": "OD1" <-> "OD2" Residue "F3 GLU 50": "OE1" <-> "OE2" Residue "F3 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 68": "OE1" <-> "OE2" Residue "F3 GLU 87": "OE1" <-> "OE2" Residue "F3 ASP 111": "OD1" <-> "OD2" Residue "F3 GLU 170": "OE1" <-> "OE2" Residue "F3 ASP 173": "OD1" <-> "OD2" Residue "F3 ASP 180": "OD1" <-> "OD2" Residue "F3 GLU 187": "OE1" <-> "OE2" Residue "F3 GLU 188": "OE1" <-> "OE2" Residue "F3 ASP 219": "OD1" <-> "OD2" Residue "F3 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 GLU 342": "OE1" <-> "OE2" Residue "F3 GLU 344": "OE1" <-> "OE2" Residue "F3 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F3 ASP 355": "OD1" <-> "OD2" Residue "F3 GLU 358": "OE1" <-> "OE2" Residue "F3 ASP 365": "OD1" <-> "OD2" Residue "F3 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 GLU 35": "OE1" <-> "OE2" Residue "F4 ASP 44": "OD1" <-> "OD2" Residue "F4 GLU 50": "OE1" <-> "OE2" Residue "F4 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 GLU 68": "OE1" <-> "OE2" Residue "F4 GLU 87": "OE1" <-> "OE2" Residue "F4 ASP 111": "OD1" <-> "OD2" Residue "F4 GLU 170": "OE1" <-> "OE2" Residue "F4 ASP 173": "OD1" <-> "OD2" Residue "F4 ASP 180": "OD1" <-> "OD2" Residue "F4 GLU 187": "OE1" <-> "OE2" Residue "F4 GLU 188": "OE1" <-> "OE2" Residue "F4 ASP 219": "OD1" <-> "OD2" Residue "F4 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 GLU 342": "OE1" <-> "OE2" Residue "F4 GLU 344": "OE1" <-> "OE2" Residue "F4 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F4 ASP 355": "OD1" <-> "OD2" Residue "F4 GLU 358": "OE1" <-> "OE2" Residue "F4 ASP 365": "OD1" <-> "OD2" Residue "F4 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 GLU 35": "OE1" <-> "OE2" Residue "F5 ASP 44": "OD1" <-> "OD2" Residue "F5 GLU 50": "OE1" <-> "OE2" Residue "F5 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 GLU 68": "OE1" <-> "OE2" Residue "F5 GLU 87": "OE1" <-> "OE2" Residue "F5 ASP 111": "OD1" <-> "OD2" Residue "F5 GLU 170": "OE1" <-> "OE2" Residue "F5 ASP 173": "OD1" <-> "OD2" Residue "F5 ASP 180": "OD1" <-> "OD2" Residue "F5 GLU 187": "OE1" <-> "OE2" Residue "F5 GLU 188": "OE1" <-> "OE2" Residue "F5 ASP 219": "OD1" <-> "OD2" Residue "F5 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 GLU 342": "OE1" <-> "OE2" Residue "F5 GLU 344": "OE1" <-> "OE2" Residue "F5 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F5 ASP 355": "OD1" <-> "OD2" Residue "F5 GLU 358": "OE1" <-> "OE2" Residue "F5 ASP 365": "OD1" <-> "OD2" Residue "F5 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13750 Number of models: 1 Model: "" Number of chains: 5 Chain: "F1" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "F2" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "F3" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "F4" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Chain: "F5" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 30, 'TRANS': 322} Time building chain proxies: 7.27, per 1000 atoms: 0.53 Number of scatterers: 13750 At special positions: 0 Unit cell: (140.8, 136.4, 90.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2675 8.00 N 2300 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYSF1 19 " - pdb=" SG CYSF2 114 " distance=2.05 Simple disulfide: pdb=" SG CYSF1 114 " - pdb=" SG CYSF5 19 " distance=2.05 Simple disulfide: pdb=" SG CYSF2 19 " - pdb=" SG CYSF3 114 " distance=2.00 Simple disulfide: pdb=" SG CYSF3 19 " - pdb=" SG CYSF4 114 " distance=2.04 Simple disulfide: pdb=" SG CYSF4 19 " - pdb=" SG CYSF5 114 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 5.18 Conformation dependent library (CDL) restraints added in 2.6 seconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 25 sheets defined 12.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'F1' and resid 33 through 39 Processing helix chain 'F1' and resid 91 through 95 Processing helix chain 'F1' and resid 131 through 137 Processing helix chain 'F1' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF1 196 " --> pdb=" O THRF1 192 " (cutoff:3.500A) Processing helix chain 'F1' and resid 202 through 207 Processing helix chain 'F1' and resid 322 through 333 removed outlier: 4.084A pdb=" N SERF1 326 " --> pdb=" O ALAF1 322 " (cutoff:3.500A) Processing helix chain 'F2' and resid 33 through 39 Processing helix chain 'F2' and resid 91 through 95 Processing helix chain 'F2' and resid 131 through 137 Processing helix chain 'F2' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF2 196 " --> pdb=" O THRF2 192 " (cutoff:3.500A) Processing helix chain 'F2' and resid 202 through 207 Processing helix chain 'F2' and resid 322 through 333 removed outlier: 4.083A pdb=" N SERF2 326 " --> pdb=" O ALAF2 322 " (cutoff:3.500A) Processing helix chain 'F3' and resid 33 through 39 Processing helix chain 'F3' and resid 91 through 95 Processing helix chain 'F3' and resid 131 through 137 Processing helix chain 'F3' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF3 196 " --> pdb=" O THRF3 192 " (cutoff:3.500A) Processing helix chain 'F3' and resid 202 through 207 Processing helix chain 'F3' and resid 322 through 333 removed outlier: 4.084A pdb=" N SERF3 326 " --> pdb=" O ALAF3 322 " (cutoff:3.500A) Processing helix chain 'F4' and resid 33 through 39 Processing helix chain 'F4' and resid 91 through 95 Processing helix chain 'F4' and resid 131 through 137 Processing helix chain 'F4' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF4 196 " --> pdb=" O THRF4 192 " (cutoff:3.500A) Processing helix chain 'F4' and resid 202 through 207 Processing helix chain 'F4' and resid 322 through 333 removed outlier: 4.084A pdb=" N SERF4 326 " --> pdb=" O ALAF4 322 " (cutoff:3.500A) Processing helix chain 'F5' and resid 33 through 39 Processing helix chain 'F5' and resid 91 through 95 Processing helix chain 'F5' and resid 131 through 137 Processing helix chain 'F5' and resid 192 through 197 removed outlier: 3.527A pdb=" N ILEF5 196 " --> pdb=" O THRF5 192 " (cutoff:3.500A) Processing helix chain 'F5' and resid 202 through 207 Processing helix chain 'F5' and resid 322 through 333 removed outlier: 4.083A pdb=" N SERF5 326 " --> pdb=" O ALAF5 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F1' and resid 47 through 53 removed outlier: 6.499A pdb=" N TYRF1 305 " --> pdb=" O THRF1 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRF1 127 " --> pdb=" O TYRF1 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF1 307 " --> pdb=" O VALF1 125 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VALF1 125 " --> pdb=" O LYSF1 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRF1 309 " --> pdb=" O VALF1 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F1' and resid 99 through 104 removed outlier: 6.625A pdb=" N ARGF1 300 " --> pdb=" O METF1 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F1' and resid 99 through 104 Processing sheet with id=AA4, first strand: chain 'F1' and resid 144 through 146 removed outlier: 6.496A pdb=" N ILEF1 153 " --> pdb=" O PROF1 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F1' and resid 213 through 215 Processing sheet with id=AA6, first strand: chain 'F1' and resid 252 through 256 Processing sheet with id=AA7, first strand: chain 'F1' and resid 252 through 256 removed outlier: 6.625A pdb=" N ARGF2 300 " --> pdb=" O METF2 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F2' and resid 47 through 53 removed outlier: 6.500A pdb=" N TYRF2 305 " --> pdb=" O THRF2 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRF2 127 " --> pdb=" O TYRF2 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF2 307 " --> pdb=" O VALF2 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALF2 125 " --> pdb=" O LYSF2 307 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THRF2 309 " --> pdb=" O VALF2 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F2' and resid 144 through 146 removed outlier: 6.496A pdb=" N ILEF2 153 " --> pdb=" O PROF2 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F2' and resid 213 through 215 Processing sheet with id=AB2, first strand: chain 'F2' and resid 252 through 256 Processing sheet with id=AB3, first strand: chain 'F2' and resid 252 through 256 removed outlier: 6.625A pdb=" N ARGF3 300 " --> pdb=" O METF3 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F3' and resid 47 through 53 removed outlier: 6.500A pdb=" N TYRF3 305 " --> pdb=" O THRF3 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THRF3 127 " --> pdb=" O TYRF3 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF3 307 " --> pdb=" O VALF3 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALF3 125 " --> pdb=" O LYSF3 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRF3 309 " --> pdb=" O VALF3 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F3' and resid 144 through 146 removed outlier: 6.495A pdb=" N ILEF3 153 " --> pdb=" O PROF3 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F3' and resid 213 through 215 Processing sheet with id=AB7, first strand: chain 'F3' and resid 252 through 256 Processing sheet with id=AB8, first strand: chain 'F3' and resid 252 through 256 removed outlier: 6.625A pdb=" N ARGF4 300 " --> pdb=" O METF4 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F4' and resid 47 through 53 removed outlier: 6.499A pdb=" N TYRF4 305 " --> pdb=" O THRF4 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRF4 127 " --> pdb=" O TYRF4 305 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYSF4 307 " --> pdb=" O VALF4 125 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VALF4 125 " --> pdb=" O LYSF4 307 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THRF4 309 " --> pdb=" O VALF4 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F4' and resid 144 through 146 removed outlier: 6.495A pdb=" N ILEF4 153 " --> pdb=" O PROF4 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F4' and resid 213 through 215 Processing sheet with id=AC3, first strand: chain 'F4' and resid 252 through 256 Processing sheet with id=AC4, first strand: chain 'F4' and resid 252 through 256 removed outlier: 6.626A pdb=" N ARGF5 300 " --> pdb=" O METF5 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F5' and resid 47 through 53 removed outlier: 6.499A pdb=" N TYRF5 305 " --> pdb=" O THRF5 127 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THRF5 127 " --> pdb=" O TYRF5 305 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSF5 307 " --> pdb=" O VALF5 125 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VALF5 125 " --> pdb=" O LYSF5 307 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THRF5 309 " --> pdb=" O VALF5 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F5' and resid 144 through 146 removed outlier: 6.495A pdb=" N ILEF5 153 " --> pdb=" O PROF5 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F5' and resid 213 through 215 441 hydrogen bonds defined for protein. 1008 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: 3.99 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4515 1.34 - 1.46: 2650 1.46 - 1.58: 6785 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14090 Sorted by residual: bond pdb=" CA GLNF4 71 " pdb=" C GLNF4 71 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.10e+00 bond pdb=" CA GLNF2 71 " pdb=" C GLNF2 71 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.05e+00 bond pdb=" CA GLNF1 71 " pdb=" C GLNF1 71 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.94e+00 bond pdb=" CA GLNF5 71 " pdb=" C GLNF5 71 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.84e+00 bond pdb=" CA GLNF3 71 " pdb=" C GLNF3 71 " ideal model delta sigma weight residual 1.532 1.520 0.013 9.60e-03 1.09e+04 1.78e+00 ... (remaining 14085 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.53: 467 105.53 - 112.66: 7494 112.66 - 119.78: 4494 119.78 - 126.90: 6524 126.90 - 134.02: 251 Bond angle restraints: 19230 Sorted by residual: angle pdb=" N GLYF5 275 " pdb=" CA GLYF5 275 " pdb=" C GLYF5 275 " ideal model delta sigma weight residual 113.18 106.43 6.75 2.37e+00 1.78e-01 8.12e+00 angle pdb=" N GLYF4 275 " pdb=" CA GLYF4 275 " pdb=" C GLYF4 275 " ideal model delta sigma weight residual 113.18 106.44 6.74 2.37e+00 1.78e-01 8.10e+00 angle pdb=" N GLYF1 275 " pdb=" CA GLYF1 275 " pdb=" C GLYF1 275 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.07e+00 angle pdb=" N GLYF3 275 " pdb=" CA GLYF3 275 " pdb=" C GLYF3 275 " ideal model delta sigma weight residual 113.18 106.45 6.73 2.37e+00 1.78e-01 8.06e+00 angle pdb=" N GLYF2 275 " pdb=" CA GLYF2 275 " pdb=" C GLYF2 275 " ideal model delta sigma weight residual 113.18 106.46 6.72 2.37e+00 1.78e-01 8.04e+00 ... (remaining 19225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 7219 16.57 - 33.15: 822 33.15 - 49.72: 299 49.72 - 66.30: 155 66.30 - 82.87: 25 Dihedral angle restraints: 8520 sinusoidal: 3475 harmonic: 5045 Sorted by residual: dihedral pdb=" CA METF2 321 " pdb=" C METF2 321 " pdb=" N ALAF2 322 " pdb=" CA ALAF2 322 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA METF3 321 " pdb=" C METF3 321 " pdb=" N ALAF3 322 " pdb=" CA ALAF3 322 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA METF1 321 " pdb=" C METF1 321 " pdb=" N ALAF1 322 " pdb=" CA ALAF1 322 " ideal model delta harmonic sigma weight residual 180.00 153.55 26.45 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1017 0.028 - 0.056: 735 0.056 - 0.084: 189 0.084 - 0.112: 180 0.112 - 0.140: 34 Chirality restraints: 2155 Sorted by residual: chirality pdb=" CA THRF4 62 " pdb=" N THRF4 62 " pdb=" C THRF4 62 " pdb=" CB THRF4 62 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA THRF5 62 " pdb=" N THRF5 62 " pdb=" C THRF5 62 " pdb=" CB THRF5 62 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA THRF2 62 " pdb=" N THRF2 62 " pdb=" C THRF2 62 " pdb=" CB THRF2 62 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2152 not shown) Planarity restraints: 2510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SERF3 89 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PROF3 90 " -0.100 5.00e-02 4.00e+02 pdb=" CA PROF3 90 " 0.030 5.00e-02 4.00e+02 pdb=" CD PROF3 90 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF5 89 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PROF5 90 " 0.100 5.00e-02 4.00e+02 pdb=" CA PROF5 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PROF5 90 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SERF4 89 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PROF4 90 " 0.099 5.00e-02 4.00e+02 pdb=" CA PROF4 90 " -0.030 5.00e-02 4.00e+02 pdb=" CD PROF4 90 " -0.032 5.00e-02 4.00e+02 ... (remaining 2507 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2782 2.77 - 3.30: 11589 3.30 - 3.84: 22479 3.84 - 4.37: 27773 4.37 - 4.90: 46427 Nonbonded interactions: 111050 Sorted by model distance: nonbonded pdb=" O LYSF5 143 " pdb=" OG1 THRF5 155 " model vdw 2.240 2.440 nonbonded pdb=" O LYSF2 143 " pdb=" OG1 THRF2 155 " model vdw 2.241 2.440 nonbonded pdb=" O LYSF4 143 " pdb=" OG1 THRF4 155 " model vdw 2.241 2.440 nonbonded pdb=" O LYSF3 143 " pdb=" OG1 THRF3 155 " model vdw 2.241 2.440 nonbonded pdb=" O LYSF1 143 " pdb=" OG1 THRF1 155 " model vdw 2.241 2.440 ... (remaining 111045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F1' selection = chain 'F2' selection = chain 'F3' selection = chain 'F4' selection = chain 'F5' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 6.590 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.850 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.038 14090 Z= 0.329 Angle : 0.773 6.754 19230 Z= 0.437 Chirality : 0.046 0.140 2155 Planarity : 0.006 0.058 2510 Dihedral : 18.357 82.870 5285 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.64 % Favored : 91.79 % Rotamer: Outliers : 12.54 % Allowed : 18.01 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.17), residues: 1755 helix: -4.73 (0.12), residues: 120 sheet: -0.84 (0.23), residues: 455 loop : -3.05 (0.15), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPF5 299 HIS 0.003 0.001 HISF4 139 PHE 0.015 0.002 PHEF3 306 TYR 0.011 0.001 TYRF5 239 ARG 0.006 0.001 ARGF3 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 314 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F1 79 ILE cc_start: 0.6502 (OUTLIER) cc_final: 0.6228 (mt) REVERT: F1 91 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6497 (tp30) REVERT: F1 93 ASN cc_start: 0.8085 (p0) cc_final: 0.7812 (p0) REVERT: F1 158 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F1 188 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: F1 204 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8014 (mttt) REVERT: F1 215 LYS cc_start: 0.8294 (mttm) cc_final: 0.7949 (mtpt) REVERT: F1 254 GLN cc_start: 0.8330 (mt0) cc_final: 0.8125 (mp10) REVERT: F1 292 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7616 (mtt180) REVERT: F1 316 LYS cc_start: 0.6248 (mttp) cc_final: 0.5148 (mmtm) REVERT: F2 91 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6448 (tp30) REVERT: F2 111 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7082 (m-30) REVERT: F2 112 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8298 (mm) REVERT: F2 158 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7922 (mt-10) REVERT: F2 196 ILE cc_start: 0.8949 (mm) cc_final: 0.8712 (mp) REVERT: F2 215 LYS cc_start: 0.8268 (mttm) cc_final: 0.8040 (mttp) REVERT: F2 292 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: F2 316 LYS cc_start: 0.6095 (mttp) cc_final: 0.4970 (mmtm) REVERT: F3 21 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7522 (ttm170) REVERT: F3 47 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8648 (m) REVERT: F3 80 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7082 (m-40) REVERT: F3 111 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: F3 117 LEU cc_start: 0.8336 (tp) cc_final: 0.8126 (tp) REVERT: F3 151 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8091 (mttm) REVERT: F3 215 LYS cc_start: 0.8195 (mttm) cc_final: 0.7890 (mtpt) REVERT: F3 221 MET cc_start: 0.8389 (mmm) cc_final: 0.8178 (mmm) REVERT: F3 254 GLN cc_start: 0.8274 (mt0) cc_final: 0.8035 (mp10) REVERT: F3 257 ASN cc_start: 0.7807 (t0) cc_final: 0.7558 (t0) REVERT: F3 266 GLU cc_start: 0.7967 (mp0) cc_final: 0.7422 (tt0) REVERT: F3 292 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7871 (mtt180) REVERT: F3 316 LYS cc_start: 0.5997 (mttp) cc_final: 0.4915 (mmtm) REVERT: F3 341 MET cc_start: 0.9043 (mmt) cc_final: 0.8814 (mmt) REVERT: F4 91 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6504 (tp30) REVERT: F4 111 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: F4 143 LYS cc_start: 0.8326 (tttt) cc_final: 0.8043 (tttm) REVERT: F4 158 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7899 (mt-10) REVERT: F4 187 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7867 (mt-10) REVERT: F4 316 LYS cc_start: 0.6200 (mttp) cc_final: 0.5151 (mmtm) REVERT: F4 341 MET cc_start: 0.8946 (mmt) cc_final: 0.7919 (mmt) REVERT: F5 91 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6437 (tp30) REVERT: F5 111 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7129 (m-30) REVERT: F5 112 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8189 (mm) REVERT: F5 143 LYS cc_start: 0.8232 (tttt) cc_final: 0.7968 (ttmt) REVERT: F5 215 LYS cc_start: 0.8359 (mttm) cc_final: 0.7941 (mttt) REVERT: F5 257 ASN cc_start: 0.7987 (t0) cc_final: 0.7772 (t0) REVERT: F5 292 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7868 (mtt180) REVERT: F5 316 LYS cc_start: 0.6225 (mttp) cc_final: 0.5115 (tptt) outliers start: 195 outliers final: 33 residues processed: 435 average time/residue: 1.2173 time to fit residues: 578.4754 Evaluate side-chains 307 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 79 ILE Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 91 GLU Chi-restraints excluded: chain F1 residue 112 LEU Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 188 GLU Chi-restraints excluded: chain F1 residue 217 ASP Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 292 ARG Chi-restraints excluded: chain F1 residue 367 THR Chi-restraints excluded: chain F1 residue 370 VAL Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 91 GLU Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 112 LEU Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 292 ARG Chi-restraints excluded: chain F2 residue 367 THR Chi-restraints excluded: chain F3 residue 21 ARG Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 44 ASP Chi-restraints excluded: chain F3 residue 47 THR Chi-restraints excluded: chain F3 residue 68 GLU Chi-restraints excluded: chain F3 residue 80 ASN Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 110 GLU Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 151 LYS Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 217 ASP Chi-restraints excluded: chain F3 residue 292 ARG Chi-restraints excluded: chain F3 residue 367 THR Chi-restraints excluded: chain F3 residue 370 VAL Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 71 GLN Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 91 GLU Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 112 LEU Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 367 THR Chi-restraints excluded: chain F4 residue 370 VAL Chi-restraints excluded: chain F5 residue 71 GLN Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 91 GLU Chi-restraints excluded: chain F5 residue 111 ASP Chi-restraints excluded: chain F5 residue 112 LEU Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 292 ARG Chi-restraints excluded: chain F5 residue 367 THR Chi-restraints excluded: chain F5 residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 54 ASN F1 118 GLN F1 142 ASN F1 149 ASN F1 163 HIS F1 254 GLN F1 339 GLN F1 347 GLN F2 54 ASN F2 118 GLN F2 142 ASN F2 163 HIS F2 206 GLN F2 257 ASN F2 339 GLN F2 347 GLN F3 54 ASN ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 118 GLN F3 142 ASN F3 163 HIS F3 206 GLN F3 254 GLN F3 257 ASN F3 339 GLN F3 347 GLN F4 54 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F4 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 118 GLN F4 142 ASN F4 163 HIS F4 206 GLN F4 257 ASN F4 339 GLN F4 347 GLN F5 54 ASN ** F5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 80 ASN ** F5 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F5 118 GLN F5 142 ASN F5 163 HIS F5 206 GLN F5 257 ASN F5 339 GLN F5 347 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14090 Z= 0.350 Angle : 0.694 8.088 19230 Z= 0.350 Chirality : 0.046 0.137 2155 Planarity : 0.006 0.047 2510 Dihedral : 10.347 93.838 1992 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 8.42 % Allowed : 21.16 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.18), residues: 1755 helix: -2.90 (0.43), residues: 120 sheet: -0.17 (0.24), residues: 450 loop : -2.55 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPF1 299 HIS 0.005 0.001 HISF4 297 PHE 0.017 0.003 PHEF2 306 TYR 0.018 0.002 TYRF1 239 ARG 0.005 0.001 ARGF1 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 250 time to evaluate : 1.548 Fit side-chains REVERT: F1 158 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7858 (mt-10) REVERT: F1 187 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: F1 215 LYS cc_start: 0.8467 (mttm) cc_final: 0.8261 (mttp) REVERT: F1 254 GLN cc_start: 0.8330 (mt0) cc_final: 0.8120 (mp10) REVERT: F1 316 LYS cc_start: 0.6410 (mttp) cc_final: 0.5335 (mmtm) REVERT: F2 111 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: F2 158 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7985 (mt-10) REVERT: F2 215 LYS cc_start: 0.8425 (mttm) cc_final: 0.8212 (mtpt) REVERT: F2 292 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7548 (mtt180) REVERT: F2 316 LYS cc_start: 0.6056 (mttp) cc_final: 0.4904 (mmtm) REVERT: F2 337 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6341 (mp-120) REVERT: F3 21 ARG cc_start: 0.7757 (mmp80) cc_final: 0.7437 (mmp-170) REVERT: F3 111 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6815 (m-30) REVERT: F3 158 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8023 (mt-10) REVERT: F3 205 ASP cc_start: 0.8132 (m-30) cc_final: 0.7830 (m-30) REVERT: F3 286 MET cc_start: 0.8538 (mmm) cc_final: 0.8336 (mmm) REVERT: F3 316 LYS cc_start: 0.6093 (mttp) cc_final: 0.4905 (mmtm) REVERT: F3 337 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6195 (mt0) REVERT: F4 57 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7105 (mmm) REVERT: F4 111 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: F4 143 LYS cc_start: 0.8262 (tttt) cc_final: 0.8050 (tttm) REVERT: F4 158 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8022 (mt-10) REVERT: F4 184 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8542 (mtmt) REVERT: F4 316 LYS cc_start: 0.6140 (mttp) cc_final: 0.5145 (mmtm) REVERT: F4 337 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6421 (mt0) REVERT: F4 341 MET cc_start: 0.8933 (mmt) cc_final: 0.7832 (mmt) REVERT: F5 111 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: F5 143 LYS cc_start: 0.8238 (tttt) cc_final: 0.7971 (ttmt) REVERT: F5 187 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7571 (mm-30) REVERT: F5 316 LYS cc_start: 0.6224 (mttp) cc_final: 0.5120 (tptt) outliers start: 131 outliers final: 54 residues processed: 331 average time/residue: 1.1167 time to fit residues: 406.4931 Evaluate side-chains 293 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 228 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 113 THR Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 187 GLU Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 124 SER Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 260 THR Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 337 GLN Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 57 MET Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 211 ILE Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 310 LEU Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 215 LYS Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 319 TYR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F4 residue 357 THR Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 111 ASP Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 207 VAL Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 319 TYR Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.0570 chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 92 ASN F2 92 ASN ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 206 GLN F3 254 GLN F4 345 ASN F5 92 ASN F5 254 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14090 Z= 0.183 Angle : 0.571 6.231 19230 Z= 0.286 Chirality : 0.042 0.127 2155 Planarity : 0.005 0.040 2510 Dihedral : 6.566 59.538 1907 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 5.27 % Allowed : 25.21 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.19), residues: 1755 helix: -1.33 (0.54), residues: 85 sheet: 0.11 (0.24), residues: 450 loop : -2.11 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPF1 299 HIS 0.003 0.001 HISF4 228 PHE 0.011 0.002 PHEF3 255 TYR 0.010 0.001 TYRF4 239 ARG 0.002 0.000 ARGF4 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 251 time to evaluate : 1.675 Fit side-chains REVERT: F1 158 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7760 (mt-10) REVERT: F1 199 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8177 (mptt) REVERT: F1 316 LYS cc_start: 0.6203 (mttp) cc_final: 0.5191 (mmtm) REVERT: F2 111 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: F2 158 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F2 308 ILE cc_start: 0.9048 (mp) cc_final: 0.8697 (mp) REVERT: F2 316 LYS cc_start: 0.5991 (mttp) cc_final: 0.4898 (mmtm) REVERT: F3 100 MET cc_start: 0.8804 (ppp) cc_final: 0.8580 (OUTLIER) REVERT: F3 111 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6805 (m-30) REVERT: F3 158 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7885 (mt-10) REVERT: F3 316 LYS cc_start: 0.5924 (mttp) cc_final: 0.4824 (mmtm) REVERT: F3 337 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6139 (mt0) REVERT: F4 57 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6822 (mmm) REVERT: F4 111 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.6853 (m-30) REVERT: F4 143 LYS cc_start: 0.8222 (tttt) cc_final: 0.7942 (tttm) REVERT: F4 158 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7968 (mt-10) REVERT: F4 316 LYS cc_start: 0.6074 (mttp) cc_final: 0.5115 (mmtm) REVERT: F4 321 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5550 (mtp) REVERT: F4 341 MET cc_start: 0.8951 (mmt) cc_final: 0.7733 (mmt) REVERT: F5 111 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6870 (m-30) REVERT: F5 143 LYS cc_start: 0.8242 (tttt) cc_final: 0.8001 (ttmt) REVERT: F5 187 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: F5 208 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7998 (tt) REVERT: F5 316 LYS cc_start: 0.6194 (mttp) cc_final: 0.5117 (tptt) outliers start: 82 outliers final: 25 residues processed: 304 average time/residue: 1.1245 time to fit residues: 376.5667 Evaluate side-chains 266 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F2 residue 111 ASP Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 112 LEU Chi-restraints excluded: chain F3 residue 113 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 199 LYS Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 208 LEU Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 282 CYS Chi-restraints excluded: chain F4 residue 319 TYR Chi-restraints excluded: chain F4 residue 321 MET Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 111 ASP Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 282 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 149 ASN ** F2 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 206 GLN F3 254 GLN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 92 ASN F4 242 ASN F4 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14090 Z= 0.210 Angle : 0.577 6.037 19230 Z= 0.288 Chirality : 0.042 0.126 2155 Planarity : 0.005 0.037 2510 Dihedral : 6.170 58.849 1902 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 6.24 % Allowed : 24.69 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1755 helix: -0.68 (0.52), residues: 85 sheet: 0.29 (0.24), residues: 450 loop : -1.92 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPF5 299 HIS 0.003 0.001 HISF4 297 PHE 0.012 0.002 PHEF2 306 TYR 0.012 0.001 TYRF1 239 ARG 0.003 0.000 ARGF4 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 242 time to evaluate : 1.571 Fit side-chains REVERT: F1 57 MET cc_start: 0.7187 (mtp) cc_final: 0.6922 (mtp) REVERT: F1 158 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7818 (mt-10) REVERT: F1 199 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8166 (mptt) REVERT: F1 316 LYS cc_start: 0.6273 (mttp) cc_final: 0.5208 (mmtm) REVERT: F2 57 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6288 (ttm) REVERT: F2 158 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7964 (mt-10) REVERT: F2 308 ILE cc_start: 0.9055 (mp) cc_final: 0.8691 (mp) REVERT: F2 316 LYS cc_start: 0.6000 (mttp) cc_final: 0.4883 (mmtm) REVERT: F3 111 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6793 (m-30) REVERT: F3 158 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7910 (mt-10) REVERT: F3 187 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7906 (mp0) REVERT: F3 205 ASP cc_start: 0.8015 (m-30) cc_final: 0.7716 (m-30) REVERT: F3 316 LYS cc_start: 0.5948 (mttp) cc_final: 0.4812 (mmtm) REVERT: F3 337 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6115 (mt0) REVERT: F4 57 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6963 (mmm) REVERT: F4 111 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.6723 (m-30) REVERT: F4 158 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8006 (mt-10) REVERT: F4 184 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8483 (mtmt) REVERT: F4 316 LYS cc_start: 0.6116 (mttp) cc_final: 0.5112 (mmtm) REVERT: F4 337 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6597 (mt0) REVERT: F4 363 ASP cc_start: 0.7629 (t0) cc_final: 0.7426 (t0) REVERT: F5 143 LYS cc_start: 0.8168 (tttt) cc_final: 0.7928 (ttmt) REVERT: F5 208 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8150 (tt) REVERT: F5 316 LYS cc_start: 0.6166 (mttp) cc_final: 0.5058 (tptt) outliers start: 97 outliers final: 54 residues processed: 299 average time/residue: 1.1652 time to fit residues: 382.9298 Evaluate side-chains 293 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 230 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 215 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 124 SER Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 260 THR Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 199 LYS Chi-restraints excluded: chain F3 residue 206 GLN Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F3 residue 324 LEU Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 83 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 111 ASP Chi-restraints excluded: chain F4 residue 113 THR Chi-restraints excluded: chain F4 residue 146 ASP Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 319 TYR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 0.0970 chunk 151 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 149 ASN F1 345 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 254 GLN F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 161 GLN F4 242 ASN F4 345 ASN F5 254 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14090 Z= 0.286 Angle : 0.623 6.140 19230 Z= 0.311 Chirality : 0.044 0.130 2155 Planarity : 0.005 0.038 2510 Dihedral : 6.050 57.723 1898 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.17 % Allowed : 25.21 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.19), residues: 1755 helix: -0.03 (0.57), residues: 85 sheet: 0.40 (0.24), residues: 450 loop : -1.90 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPF3 299 HIS 0.004 0.001 HISF5 298 PHE 0.016 0.003 PHEF2 306 TYR 0.015 0.002 TYRF4 239 ARG 0.003 0.001 ARGF4 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 227 time to evaluate : 1.847 Fit side-chains REVERT: F1 158 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7871 (mt-10) REVERT: F1 316 LYS cc_start: 0.6300 (mttp) cc_final: 0.5238 (mmtm) REVERT: F2 57 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6389 (ttm) REVERT: F2 146 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6445 (m-30) REVERT: F2 158 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7982 (mt-10) REVERT: F2 289 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7991 (ttt180) REVERT: F2 316 LYS cc_start: 0.6127 (mttp) cc_final: 0.4985 (mmtm) REVERT: F3 111 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: F3 119 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8363 (ptm) REVERT: F3 316 LYS cc_start: 0.5882 (mttp) cc_final: 0.4700 (mmtm) REVERT: F3 337 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6139 (mt0) REVERT: F4 57 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7013 (mmm) REVERT: F4 158 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8050 (mt-10) REVERT: F4 184 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8504 (mtmt) REVERT: F4 316 LYS cc_start: 0.6148 (mttp) cc_final: 0.5077 (mmtm) REVERT: F4 337 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6630 (mt0) REVERT: F5 57 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6437 (ttm) REVERT: F5 143 LYS cc_start: 0.8169 (tttt) cc_final: 0.7907 (ttmt) REVERT: F5 208 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8127 (tt) REVERT: F5 316 LYS cc_start: 0.6279 (mttp) cc_final: 0.5138 (tptt) outliers start: 96 outliers final: 66 residues processed: 288 average time/residue: 1.2016 time to fit residues: 379.6061 Evaluate side-chains 300 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 224 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 31 LYS Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 124 SER Chi-restraints excluded: chain F2 residue 146 ASP Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 154 SER Chi-restraints excluded: chain F2 residue 170 GLU Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 260 THR Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 111 ASP Chi-restraints excluded: chain F3 residue 112 LEU Chi-restraints excluded: chain F3 residue 113 THR Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 170 GLU Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 211 ILE Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F3 residue 350 GLU Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 83 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 113 THR Chi-restraints excluded: chain F4 residue 146 ASP Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 154 SER Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 215 LYS Chi-restraints excluded: chain F4 residue 253 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 319 TYR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 211 ILE Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.5980 chunk 152 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 149 ASN F1 345 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 254 GLN F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 161 GLN F4 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14090 Z= 0.234 Angle : 0.587 5.689 19230 Z= 0.294 Chirality : 0.043 0.126 2155 Planarity : 0.005 0.036 2510 Dihedral : 5.674 58.790 1896 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 5.92 % Allowed : 24.95 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1755 helix: 0.34 (0.59), residues: 85 sheet: 0.51 (0.25), residues: 450 loop : -1.82 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPF1 299 HIS 0.003 0.001 HISF4 297 PHE 0.013 0.002 PHEF2 306 TYR 0.014 0.001 TYRF4 239 ARG 0.002 0.000 ARGF4 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 231 time to evaluate : 1.603 Fit side-chains REVERT: F1 158 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7820 (mt-10) REVERT: F1 316 LYS cc_start: 0.6286 (mttp) cc_final: 0.5251 (mmtm) REVERT: F2 57 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6328 (ttm) REVERT: F2 158 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7952 (mt-10) REVERT: F2 289 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8063 (ttp80) REVERT: F2 316 LYS cc_start: 0.5917 (mttp) cc_final: 0.4846 (tppt) REVERT: F3 119 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8330 (ptm) REVERT: F3 292 ARG cc_start: 0.7954 (ttt180) cc_final: 0.7707 (mtt180) REVERT: F3 316 LYS cc_start: 0.5848 (mttp) cc_final: 0.4676 (mmtm) REVERT: F3 337 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6227 (mt0) REVERT: F3 366 MET cc_start: 0.6121 (mmp) cc_final: 0.5859 (mmm) REVERT: F4 57 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6968 (mmm) REVERT: F4 158 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8022 (mt-10) REVERT: F4 184 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8492 (mtmt) REVERT: F4 316 LYS cc_start: 0.6145 (mttp) cc_final: 0.5131 (mmtm) REVERT: F4 337 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6607 (mt0) REVERT: F5 57 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6435 (ttm) REVERT: F5 143 LYS cc_start: 0.8095 (tttt) cc_final: 0.7861 (ttmt) REVERT: F5 208 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8091 (tt) REVERT: F5 292 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7619 (ttt180) REVERT: F5 316 LYS cc_start: 0.6191 (mttp) cc_final: 0.5078 (tptt) outliers start: 92 outliers final: 59 residues processed: 289 average time/residue: 1.1268 time to fit residues: 358.0712 Evaluate side-chains 292 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 224 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 215 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 113 THR Chi-restraints excluded: chain F2 residue 124 SER Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 170 GLU Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 113 THR Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 199 LYS Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 83 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 113 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 113 THR Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 292 ARG Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 142 optimal weight: 0.0020 chunk 94 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 149 ASN F1 345 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 254 GLN F3 345 ASN F4 161 GLN F4 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14090 Z= 0.257 Angle : 0.604 5.774 19230 Z= 0.302 Chirality : 0.043 0.128 2155 Planarity : 0.005 0.036 2510 Dihedral : 5.575 58.472 1892 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 6.24 % Allowed : 25.08 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.20), residues: 1755 helix: 0.53 (0.60), residues: 85 sheet: 0.55 (0.25), residues: 450 loop : -1.77 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPF4 299 HIS 0.003 0.001 HISF5 298 PHE 0.015 0.002 PHEF2 306 TYR 0.014 0.001 TYRF4 239 ARG 0.003 0.000 ARGF3 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 223 time to evaluate : 1.731 Fit side-chains REVERT: F1 158 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7824 (mt-10) REVERT: F1 292 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7264 (mtt180) REVERT: F1 316 LYS cc_start: 0.6255 (mttp) cc_final: 0.5245 (mmtm) REVERT: F1 366 MET cc_start: 0.6472 (mmp) cc_final: 0.6182 (mmm) REVERT: F2 57 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6469 (ttm) REVERT: F2 158 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7971 (mt-10) REVERT: F2 289 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8084 (ttp80) REVERT: F2 316 LYS cc_start: 0.6033 (mttp) cc_final: 0.4931 (tppt) REVERT: F3 119 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8313 (ptm) REVERT: F3 316 LYS cc_start: 0.5918 (mttp) cc_final: 0.4681 (mmtm) REVERT: F3 337 GLN cc_start: 0.6586 (OUTLIER) cc_final: 0.6216 (mt0) REVERT: F3 366 MET cc_start: 0.6156 (mmp) cc_final: 0.5884 (mmm) REVERT: F4 57 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: F4 158 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8041 (mt-10) REVERT: F4 184 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8503 (mtmt) REVERT: F4 199 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8236 (mppt) REVERT: F4 316 LYS cc_start: 0.6156 (mttp) cc_final: 0.5136 (mmtm) REVERT: F4 337 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6655 (mt0) REVERT: F4 341 MET cc_start: 0.8935 (mmt) cc_final: 0.7821 (mmt) REVERT: F5 57 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6287 (ttm) REVERT: F5 143 LYS cc_start: 0.8142 (tttt) cc_final: 0.7887 (ttmt) REVERT: F5 208 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8121 (tt) REVERT: F5 292 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7591 (ttt180) REVERT: F5 316 LYS cc_start: 0.6206 (mttp) cc_final: 0.5094 (tptt) outliers start: 97 outliers final: 62 residues processed: 283 average time/residue: 1.1483 time to fit residues: 357.4442 Evaluate side-chains 290 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 218 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 31 LYS Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 86 THR Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 207 VAL Chi-restraints excluded: chain F1 residue 215 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 357 THR Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 86 THR Chi-restraints excluded: chain F2 residue 124 SER Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 170 GLU Chi-restraints excluded: chain F2 residue 207 VAL Chi-restraints excluded: chain F2 residue 259 LEU Chi-restraints excluded: chain F2 residue 281 SER Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 86 THR Chi-restraints excluded: chain F3 residue 113 THR Chi-restraints excluded: chain F3 residue 119 MET Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 147 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 170 GLU Chi-restraints excluded: chain F3 residue 199 LYS Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F3 residue 337 GLN Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 86 THR Chi-restraints excluded: chain F4 residue 113 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 199 LYS Chi-restraints excluded: chain F4 residue 207 VAL Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 211 ILE Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F4 residue 337 GLN Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 83 THR Chi-restraints excluded: chain F5 residue 86 THR Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 154 SER Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 208 LEU Chi-restraints excluded: chain F5 residue 211 ILE Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Chi-restraints excluded: chain F5 residue 292 ARG Chi-restraints excluded: chain F5 residue 296 VAL Chi-restraints excluded: chain F5 residue 357 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.0170 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 149 ASN ** F2 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 254 GLN F3 345 ASN ** F4 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14090 Z= 0.158 Angle : 0.525 6.138 19230 Z= 0.261 Chirality : 0.040 0.128 2155 Planarity : 0.004 0.030 2510 Dihedral : 4.936 53.791 1892 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.79 % Allowed : 27.46 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1755 helix: -0.62 (0.48), residues: 125 sheet: 0.68 (0.26), residues: 450 loop : -1.57 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPF5 299 HIS 0.002 0.001 HISF4 298 PHE 0.014 0.002 PHEF3 255 TYR 0.008 0.001 TYRF2 239 ARG 0.002 0.000 ARGF1 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 1.719 Fit side-chains REVERT: F1 85 ASP cc_start: 0.8174 (t70) cc_final: 0.7902 (t0) REVERT: F1 215 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8040 (mtpt) REVERT: F1 265 ASP cc_start: 0.7826 (p0) cc_final: 0.7522 (p0) REVERT: F1 316 LYS cc_start: 0.5763 (mttp) cc_final: 0.4885 (mmtm) REVERT: F1 366 MET cc_start: 0.6522 (mmp) cc_final: 0.6273 (mmm) REVERT: F2 57 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6794 (tpp) REVERT: F2 158 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7866 (mt-10) REVERT: F2 187 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: F2 308 ILE cc_start: 0.9019 (mp) cc_final: 0.8646 (mm) REVERT: F2 316 LYS cc_start: 0.6063 (mttp) cc_final: 0.5057 (tppt) REVERT: F3 158 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7742 (mt-10) REVERT: F3 257 ASN cc_start: 0.7087 (t0) cc_final: 0.6877 (t0) REVERT: F3 292 ARG cc_start: 0.7806 (ttt180) cc_final: 0.7511 (mtt180) REVERT: F3 316 LYS cc_start: 0.5710 (mttp) cc_final: 0.4800 (tppt) REVERT: F3 366 MET cc_start: 0.6099 (mmp) cc_final: 0.5867 (mmm) REVERT: F4 57 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6876 (mmm) REVERT: F4 147 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6485 (m) REVERT: F4 158 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7965 (mt-10) REVERT: F4 184 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8453 (mtmt) REVERT: F4 316 LYS cc_start: 0.6020 (mttp) cc_final: 0.5129 (mppt) REVERT: F4 366 MET cc_start: 0.6196 (mmp) cc_final: 0.5910 (mmt) REVERT: F5 57 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6388 (ttm) REVERT: F5 143 LYS cc_start: 0.8119 (tttt) cc_final: 0.7859 (ttmt) REVERT: F5 187 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: F5 316 LYS cc_start: 0.6058 (mttp) cc_final: 0.4899 (tppt) outliers start: 59 outliers final: 33 residues processed: 289 average time/residue: 1.1266 time to fit residues: 359.4020 Evaluate side-chains 278 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 199 LYS Chi-restraints excluded: chain F1 residue 215 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 187 GLU Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 296 VAL Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 113 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 190 VAL Chi-restraints excluded: chain F4 residue 199 LYS Chi-restraints excluded: chain F4 residue 208 LEU Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 149 ASN F1 345 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 161 GLN ** F4 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14090 Z= 0.362 Angle : 0.665 6.540 19230 Z= 0.331 Chirality : 0.045 0.135 2155 Planarity : 0.005 0.034 2510 Dihedral : 5.740 56.201 1892 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.54 % Allowed : 27.85 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1755 helix: 0.71 (0.60), residues: 85 sheet: 0.47 (0.25), residues: 460 loop : -1.64 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPF1 299 HIS 0.005 0.001 HISF1 297 PHE 0.021 0.003 PHEF2 306 TYR 0.017 0.002 TYRF4 239 ARG 0.004 0.001 ARGF1 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 1.539 Fit side-chains REVERT: F1 57 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7173 (tpp) REVERT: F1 215 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8029 (mtpt) REVERT: F1 292 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7327 (mtt180) REVERT: F1 316 LYS cc_start: 0.5908 (mttp) cc_final: 0.4997 (mmtm) REVERT: F1 366 MET cc_start: 0.6554 (mmp) cc_final: 0.6341 (mmm) REVERT: F2 158 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7994 (mt-10) REVERT: F2 289 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8025 (ptt90) REVERT: F2 316 LYS cc_start: 0.6088 (mttp) cc_final: 0.4928 (tppt) REVERT: F3 274 LYS cc_start: 0.7863 (mttt) cc_final: 0.7543 (mtpt) REVERT: F3 292 ARG cc_start: 0.7949 (ttt180) cc_final: 0.7644 (mtt180) REVERT: F3 316 LYS cc_start: 0.6007 (mttp) cc_final: 0.4708 (mmtm) REVERT: F3 337 GLN cc_start: 0.6830 (mp10) cc_final: 0.6435 (mt0) REVERT: F3 366 MET cc_start: 0.6116 (mmp) cc_final: 0.5914 (mmm) REVERT: F4 57 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6930 (mmm) REVERT: F4 158 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8097 (mt-10) REVERT: F4 184 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8407 (mtmt) REVERT: F4 199 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8237 (mppt) REVERT: F4 316 LYS cc_start: 0.6182 (mttp) cc_final: 0.5056 (mmtm) REVERT: F4 341 MET cc_start: 0.8848 (mmp) cc_final: 0.7818 (mmt) REVERT: F4 366 MET cc_start: 0.6168 (mmp) cc_final: 0.5961 (mmt) REVERT: F5 57 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6216 (ttm) REVERT: F5 143 LYS cc_start: 0.8138 (tttt) cc_final: 0.7890 (ttmt) REVERT: F5 187 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: F5 316 LYS cc_start: 0.6308 (mttp) cc_final: 0.5153 (tptt) outliers start: 55 outliers final: 38 residues processed: 271 average time/residue: 1.2968 time to fit residues: 383.3779 Evaluate side-chains 275 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 57 MET Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 147 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 215 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F1 residue 321 MET Chi-restraints excluded: chain F2 residue 36 VAL Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 113 THR Chi-restraints excluded: chain F2 residue 147 THR Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F2 residue 324 LEU Chi-restraints excluded: chain F2 residue 357 THR Chi-restraints excluded: chain F3 residue 36 VAL Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 83 THR Chi-restraints excluded: chain F3 residue 113 THR Chi-restraints excluded: chain F3 residue 146 ASP Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 207 VAL Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 281 SER Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F3 residue 319 TYR Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 57 MET Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 147 THR Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 199 LYS Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F4 residue 323 SER Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 57 MET Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 147 THR Chi-restraints excluded: chain F5 residue 187 GLU Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 281 SER Chi-restraints excluded: chain F5 residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 174 optimal weight: 0.0170 chunk 160 optimal weight: 0.0980 chunk 138 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.0470 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 149 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 242 ASN F4 345 ASN F5 254 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14090 Z= 0.163 Angle : 0.537 6.575 19230 Z= 0.267 Chirality : 0.040 0.130 2155 Planarity : 0.004 0.034 2510 Dihedral : 4.944 55.362 1892 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.25 % Allowed : 29.39 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1755 helix: -0.39 (0.49), residues: 125 sheet: 0.75 (0.26), residues: 450 loop : -1.47 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPF5 299 HIS 0.003 0.001 HISF4 298 PHE 0.016 0.001 PHEF3 255 TYR 0.009 0.001 TYRF1 319 ARG 0.003 0.000 ARGF3 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.627 Fit side-chains REVERT: F1 57 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6021 (ttm) REVERT: F1 215 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8022 (mtpt) REVERT: F1 265 ASP cc_start: 0.7849 (p0) cc_final: 0.7569 (p0) REVERT: F1 316 LYS cc_start: 0.5605 (mttp) cc_final: 0.4763 (mmtm) REVERT: F1 366 MET cc_start: 0.6440 (mmp) cc_final: 0.6186 (mmm) REVERT: F2 57 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.6805 (tpp) REVERT: F2 158 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7861 (mt-10) REVERT: F2 308 ILE cc_start: 0.9013 (mp) cc_final: 0.8660 (mm) REVERT: F2 316 LYS cc_start: 0.5687 (mttp) cc_final: 0.4771 (mmtm) REVERT: F3 158 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7726 (mt-10) REVERT: F3 292 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7540 (mtt180) REVERT: F3 316 LYS cc_start: 0.5718 (mttp) cc_final: 0.4776 (tppt) REVERT: F4 57 MET cc_start: 0.7311 (ttm) cc_final: 0.6860 (mmm) REVERT: F4 158 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7924 (mt-10) REVERT: F4 184 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8488 (mtmt) REVERT: F4 316 LYS cc_start: 0.6091 (mttp) cc_final: 0.4998 (tptt) REVERT: F5 143 LYS cc_start: 0.8121 (tttt) cc_final: 0.7867 (ttmt) REVERT: F5 316 LYS cc_start: 0.6095 (mttp) cc_final: 0.4914 (tppt) outliers start: 35 outliers final: 22 residues processed: 258 average time/residue: 1.1582 time to fit residues: 328.5076 Evaluate side-chains 255 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F1 residue 36 VAL Chi-restraints excluded: chain F1 residue 57 MET Chi-restraints excluded: chain F1 residue 67 THR Chi-restraints excluded: chain F1 residue 154 SER Chi-restraints excluded: chain F1 residue 215 LYS Chi-restraints excluded: chain F1 residue 252 VAL Chi-restraints excluded: chain F1 residue 282 CYS Chi-restraints excluded: chain F2 residue 57 MET Chi-restraints excluded: chain F2 residue 67 THR Chi-restraints excluded: chain F2 residue 113 THR Chi-restraints excluded: chain F2 residue 282 CYS Chi-restraints excluded: chain F2 residue 319 TYR Chi-restraints excluded: chain F3 residue 67 THR Chi-restraints excluded: chain F3 residue 113 THR Chi-restraints excluded: chain F3 residue 154 SER Chi-restraints excluded: chain F3 residue 170 GLU Chi-restraints excluded: chain F3 residue 259 LEU Chi-restraints excluded: chain F3 residue 282 CYS Chi-restraints excluded: chain F4 residue 36 VAL Chi-restraints excluded: chain F4 residue 67 THR Chi-restraints excluded: chain F4 residue 184 LYS Chi-restraints excluded: chain F4 residue 260 THR Chi-restraints excluded: chain F5 residue 36 VAL Chi-restraints excluded: chain F5 residue 67 THR Chi-restraints excluded: chain F5 residue 199 LYS Chi-restraints excluded: chain F5 residue 282 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 128 optimal weight: 0.0050 chunk 20 optimal weight: 0.4980 chunk 38 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1 149 ASN F1 345 ASN ** F2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 317 ASN ** F3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 345 ASN ** F4 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F4 242 ASN F4 345 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.146972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.114508 restraints weight = 13618.552| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.77 r_work: 0.2894 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14090 Z= 0.167 Angle : 0.533 6.525 19230 Z= 0.264 Chirality : 0.041 0.126 2155 Planarity : 0.004 0.028 2510 Dihedral : 4.790 50.868 1892 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.61 % Allowed : 30.29 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1755 helix: -0.25 (0.50), residues: 125 sheet: 0.64 (0.26), residues: 460 loop : -1.35 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPF5 299 HIS 0.003 0.001 HISF4 228 PHE 0.014 0.002 PHEF3 255 TYR 0.009 0.001 TYRF2 239 ARG 0.003 0.000 ARGF3 304 =============================================================================== Job complete usr+sys time: 5942.55 seconds wall clock time: 105 minutes 48.90 seconds (6348.90 seconds total)